From SG-eye's FAQ:

1) What are "Temple Issues"?

Following the split between Soka Gakkai and Nichiren Shoshu, Soka Gakkai started a campaign called "Temple Issues" to demonize Nichiren Shoshu and its High Priest Nikken Shonin. Initially "temple Issues" was used to provide a pretext for Soka Gakkai cleaving their members from the Nichiren shoshu religion they belonged to. Now this campaign is aimed at harassing Nichiren Shoshu & discouraging Soka Gakkai members thinking of re-joining Nichiren Shoshu.
Under the above Nichiren Shoshu/SG-eye definition, this website is "a temple issue site," "demonizing" Nichiren Shoshu, "discouraging" SGI members from joining Nichiren Shoshu, and "harassing" its members. That's because it responds to the horrible slanders Nichiren Shoshu promulgates about the SGI and President Ikeda, and it compares the published doctrines of Nichiren Shoshu to the Gosho of Nichiren Daishonin and shows the two sources are incompatible; while the doctrines adopted by the SGI come directly from the Gosho.

Under the Nichiren Shoshu definition, it gets to say anything it wants about the SGI, and any response is "demonizing" and "trampling our rights".

2) "Why did Soka Gakkai split from Nichiren Shoshu"?
Most of the Nichiren Shoshu/SG-eye misrepresentations and outright lies have been addressed earlier: the internal memo about the priesthood, the "deviations" of the 70s; President Ikeda's apology, his "deification", etc.

One further error in what SG-eye says here: 

When it became clear that the Nichiren Shoshu priesthood would not bend he established his own religion - registering the name Nichiren Sekaishu with the Japanese authorities and introducing new prayers, doctrines and a new object of worship to the members. 

As Soka Gakkai had become, in effect a new religion, the organisation (nb. not the members) was excommunicated and lost its qualification as a Nichiren Shoshu lay group. As the engineer of the split, Daisaku Ikeda was also excommunicated from the religion.

First of all, the Soka Gakkai is called "The Soka Gakkai". The name of the sect has not changed — nor is there a need to change it. The Gakkai has always been a separate organization from Nichiren Shoshu — legally, philosophically, in the scope of its activities. There is no need to register a new name to "establish his own religion". The name "Nichiren Sekaishu" was registered — as it was explained at the time — as preemptive, so that no one could claim the Gakkai had no legal right to use the name Nichiren.

Second, there are no "new" prayers, doctrines or object of worship — most of this has also been previously addressed. The prayers are the recitation of the Lotus Sutra and the chanting of daimoku, like always; the doctrines are those actually taught by Nichiren, which is, in a sense, "new" in that those older doctrines have supplanted the later interpretations of those doctrines by priests; and the object of worship is the Gohonzon of Nichiren, like always.

Besides those misrepresentations, the timeline presented here by SG-eye is deliberately skewed. SG-eye makes it appear that the SGI adopted a separate gongyo format, refuted the priests' doctrines, began to issue Gohonzon — and then Nikken Abe excommunicated the SGI. As has been mentioned earlier, the fact is that Nichiren Shoshu took a number of unilateral action, including denying the Gohonzon to SGI members, leading inevitably (since that was the purpose of the actions) to excommunication. Then and only then, did the SGI issue its own gongyo books (first printing in November 1992); and it wasn't until over a year after the excommunication (which occurred in November 1991) that a Reform Priest offered a Gohonzon for the Gakkai to issue its members.

3) "Have the Soka Gakkai & Soka Gakkai International (SGI) members been excommunicated"? 

No. After seven years, during which time they effectively changed religion, Soka Gakkai members lost their qualification as Nichiren Shoshu members. 
From the publication of the Chicago Nichiren Shoshu temple Myogyoji News, dated March 1992: 
TO: All Members of the Soka Gakkai 
FROM: Nichiren Shoshu Bureau of Religious Affairs

On November 28th, 1991, Nichiren Shoshu notified the Soka Gakkai organization of its expulsion from this sect.

Nichiren Shoshu maintains — and maintains even in this Notice of Excommunication — that no actual members of the SGI were expelled: they could still ask the priests to perform various ceremonies (for which, coincidentally, an offering was required, though neither the Notice nor SG-eye mention this coincidence); they could even receive Gohonzon if they joined a lay group sanctioned by the priests. In effect, however (also for some reason not mentioned), for any of this to happen, one was required to leave the SGI.

Basically, the argument they present here is that its possible, for instance, for the Chicago Bears to win the Super Bowl without any Chicago Bears players winning the Super Bowl. How can an organization be excommunicated, but no one in the organization?

It was no doubt assumed by Nikken Abe that, once this extreme step was taken, Gakkai members would finally be frightened enough for their salvation to quit in droves. It did not happen. Nor did it happen when Nichiren Shoshu notified Gakkai members that, if they accepted the SGI-issued Gohonzon in 1993-1994, they would for sure, really be excommunicated (most didn't care, assuming they'd already been excommunicated).

So in 1997, with a numeric goal set for attendance at an upcoming pilgrimage, Nichiren Shoshu tried again. They informed SGI members again that they had never been excommunicated, that they were still Nichiren Shoshu members — but now had a deadline (December 27, 1997 in the U.S.) to quit the SGI, or this time, for sure, really and truly, they'd no longer be Nichiren Shoshu members. 

To them this is still not excommunication. "If you are an SGI member, you lose your membership is Nichiren Shoshu" is not excommunication? 

It is just Nichiren Shoshu trying to lay the blame for their own actions on SGI members. "Give me your money or I'll shoot you. You won't give me your money? Then you freely chose to be shot — don't blame me."

Same thing.

4) "Can Soka Gakkai members rejoin Nichiren Shoshu?"

Yes — they can rejoin Nichiren Shoshu again if they revert to their previously held doctrines, prayers, object of worship, leave Soka Gakkai and become members of Hokkeko.
This is, perhaps, the only sub-section of the entire SG-eye website that is entirely true.

5) "Surely if we are chanting we are all practicing True Buddhism?"

The Daishonin says "there is a difference if one chants the daimoku while acting against the intent of this sutra".

Just because one is chanting Daimoku it does not mean that they are practicing the correct religion. 

That much is true — Nichiren Daishonin does say that. However: 
For example, The Daishonin says that the heart of his teachings, The Buddha & the Law are transmitted by the priesthood — Soka Gakkai denies the need for a priesthood even though the Daishonin established it to protect and hand down his teachings in Mappo. 
The fact is that Nichiren did not establish a priesthood, and his references to preserving and handing down the teachings refer not to a clerical order but to the Third Treasure of Buddhism. This is the "sangha", the community of believers. In Japanese the word "sangha" was translated to the word "priest", but in all but a few Therevada sects — and Nichiren Shoshu — it implies "monks and nuns, laymen and lay women". What he praised was the fact of handing down and preserving, and was effusive in his praise for laity who performed this function. 
Can it be that Shakyamuni Buddha or the Bodhisattvas of the Earth have entered into your body? I entrust you with the propagation of Buddhism in your province. —"The Properties of Rice," WND, p. 117; to lay believer thought to be Takahashi Rokuro Hyoe.

Abutsubo, you deserve to be called a leader of the northern province. Could it be that Bodhisattva Pure Practices has been reborn into this world as Abutsubo and visited me? How wonderful! —"On the Treasure Tower," WND, p. 300; to lay believer Abutsubo of Sado Island.

Despite all the risks involved, you traveled to Sado carrying your infant daughter, since her father, from whom you have long been separated, was not to be depended upon for her care. —"Letter to the Sage Nichimyo," WND, p. 325; to a woman who, contrary to the mores at the time, had abandoned her husband; despite this, her strong faith led the Daishonin to give her the title "Sage" — "Shonin", the same word used by Nichiren Shoshu as an honorific for its high priests.

The Daishonin's Buddhism is a dynamic, living religion because its principles and concepts can be found in, and applied to, the lives of all its individual practitioners — monks or nuns, laymen or lay women. The importance of the 3rd Treasure — whether it is called the Treasure of the Community or the Treasure of the Priest — is the act of preserving and propagating. It is never found in empty formality, such as Nichiren Shoshu's calling it (virtually alone among Buddhist sects) The Treasure of the Priesthood — which implies that so important a designation is nothing but a honorific for one who has taken clerical vows.

SG-eye continues: 

Soka Gakkai also downplays the significance of the Daigohonzon and blurs the distinction between it and any other printed or carved mandala. This is demonstrated in the changing of the second prayer in Soka Buddhism. 
Many doctrinal matters are discussed in the next section, "Guidance", so there's no need to go into them here. The silent prayers of gongyo, however, are not a doctrinal matter. They were not established by Nichiren: his only comment on the recitation of the Lotus Sutra is that it should be done, but he doesn't specify a number of times it should be read, or a format, or intermittent silent prayers. All these things are arbitrary, and in fact the silent prayers have been changed more than once by the Nichiren Shoshu priesthood.

The five silent prayers in Nichiren Shoshu traditionally thank the Buddhist deities for protection; thank and praise the Dai Gohonzon; thank and praise Nichiren, Nikko and Nichimoku and the successive High Priests; pray for worldwide propagation and for the changing of the practitioners evil karma; and offer prayers for the repose of the dead, concluding with a prayer for peace and happiness for all humanity.

The SGI-recommended silent prayers do all these things — including appreciation to the Dai Gohonzon — with the exception of thanking the successive High Priests, since we now know that many of them did nothing for which they should be thanked. 

Of course, no one can dictate what is truly in a person's heart their true "prayer." But Nichiren Shoshu has insisted that 

"the most important significance of gongyo can be found within the titles and in the meanings of the actual sentences of the silent prayers" —Overseas Bureau Chief Rev. Obayashi, August 1992 Myogyoji News, p. 5
Demanding that a certain wording is doctrinally imperative is not only hypocritical in light of the priesthood's own historic tinkering with the prayers; it makes a heartfelt offering of prayer impossible. For example, consider the Nichiren Shoshu wording of the second prayer at the time of the excommunication: 
I solemnly praise the Dai Gohonzon — the core of the Juryo Chapter of Honmon, the Supreme Law hidden in the depths of the Lotus Sutra, the inscrutable essence of the universe, the perfect fusion of kyo and chi, the entity of kuon ganjo, the entity of the Buddha of absolute freedom, the eternal manifestation of the ten worlds, the embodiment of ichinen sanzen, the Oneness of Person and Law, the Dai Gohonzon enshrined in the High Sanctuary of True Buddhism. I also give thanks for the immeasurable benefits I have received. 
In contrast to that "silent study meeting" required by Nichiren Shoshu, the Gakkai second prayer
I offer my deepest praise and most sincere appreciation to the Dai Gohonzon of the Three Great Secret Laws, which was bestowed upon the entire world.
Additionally, the introduction to the silent prayers in the Gakkai liturgy book stipulates that 
The silent prayers are intended to express our shared sense of gratitude and resolve as believers . . . it is not the specific wording of the silent prayers, but rather what we have I our minds while performing the prayers that is most important.
What is closer to the intent of "prayer"? Is it the required repetition of difficult concepts, or a suggested expression of one's own mind?

SG-eye continues: 

Soka Gakkai also seems to blur the distinction between the Daishonin's life and mission as True Buddha and our own lives. It justifies a belief that "we are the Gohonzon" by quoting, out of context, a metaphorical use of the word "Gohonzon" from the Gosho. In Nichiren Shoshu True Buddhism the Gohonzon is the life of Nichiren Daishonin towards which we practice to manifest our Buddha nature (the metaphorical "Gohonzon" within our lives).
Nichiren Daishonin says that an object of worship needs to be endowed with the spiritual qualities of the Buddha before it becomes valid. The Gakkai says that this ceremony is not necessary.

These points will be addressed in the section on "Guidance".

Many Soka Gakkai members will remember making solemn promises at their Gojukai ceremony — this is now no longer performed in the new Soka religion.
Nichiren Shoshu's insistence that the heart of Buddhism lies in ceremonies alone indicates it is far from "the true school" of the Daishonin's Buddhism.

The Gojukai ceremony is a fairly recent development. This is obvious, because in 1900, the priests were giving away specially transcribed Gohonzon to non-members who made donations, and as late as 1930, were advertising Gohonzon in the local papers around Taisekiji.

In fact, first Soka Gakkai President Makiguchi asked the priesthood to devise a ceremony to emphasize the meaning and significance of receiving the Gohonzon. In this ceremony, the new believer vowed to protect the Gohonzon, practice True Buddhism and uphold the teachings of Nichiren Shoshu. The meaning, of course, is in a lifelong commitment to practice and propagate the Daishonin's Buddhism correctly. Since the priesthood has severed whatever connection it once had to Nichiren Daishonin, its Gojukai ceremony is an empty ritual. (For many, it could be said, it was always just a ritual; how can a lifelong commitment be made by someone who is just joining, who doesn't understand yet what it is he/she is committing to? It is how one lives, not what ceremonies one participates in, that determines one's happiness). 

In short there are many different sects of Buddhism, but the Daishonin only established one — Nichiren Shoshu.
Compare that with:
 "I, Nichiren, am not the founder of any school, nor am I a latter day follower of any older school." —"The Blessings of the Lotus Sutra," WND, p. 669