Well..the "crazier" Nichiren sect is now the largest Buddhist school in the world.. go figure. But it is important to understand that there is also great diversity within the Nichiren Sect. The largest is of course the Soka Gakkai and it's estranged Order the Nicihren Shoshu. They have adopted a crude Health Wealth and Happiness format. Most everything they teach is inauthentic in terms of what Nichiren Shonin actually taught. Their most prized writings ( "Gosho") are almost all forgeries.
Most Buddhists I've heard from on the matter are of the opinion that SGI is not really Buddhist, more of a new religion, for just these reasons. The more "orthodox" Nichiren seem to have some recognition. I heard there is a statue of Nichiren at the main Tiantai temple in China (as you may know, the Tiantai sect greatly revered the Lotus Sutra).
There are many other Nichiren sects: Nichiren Shu, Kempon Hokke shu, Honmon butusryu Shu and others that are very traditional and authentic. Nichiren is disliked because he was Japanese and not Chinese and carried some national prejudices.
Disliked by whom? In terms of national prejudices, maybe he stood out in his time but after WWII I don't think any Japanese Buddhist sect is untainted. Yasutani Roshi comes to mind, who has a pervasive influence in modern Zen and who was a rabid cheerleader for Japanese imperialism (he was certainly not alone in this among Buddhist leaders).
I think Nichiren tends to raise eyebrows because his teaching is kind of... odd. The Buddha's ultimate teaching is to chant the name of a sutra, even if this practice isn't explicitly taught in the sutra itself? In Japanese? Other Japanese teachers like Shinran or Dogen had their radical moments but nothing quite so outlandish.
He famously is credited for conjuring up the Typhoon that sank the entire invading Chinese armada...
Wasn't that the Mongols?
The SGI was the lay organization for a legit Nichrien branch, the Nichiren Shoshu. They had diverged from authentic Nichiren-ism in the 1400's. They adopted a concept called "Hongaku Shi so". Everyone is the Buddha, you need only practice to bring out this inherent Buddha-hood. Lots of Japanese Buddhism was infected by this idea and you can see it all round today. When you see the metaphor " Polish the Mirror of your life to reflect your Buddhahood" it is representative of this concept.
Nichiren had a far different idea. He took the Eternal Buddha seriously and believed in his actual existence ( he was not a metaphor for the "Buddha within"). Nichiren started out as a Tendai Shu monk whom as you pointed out take the Lotus Sutra ( "Hokkeyo" jap.) as the final and supreme teaching of Buddhism.
They believe as does the Nichiren Sect that as we travel in time further and further away from the Buddha's temporal life in India, the capacity of the ordinary person to practice diminishes. At the point in time of master Tendai (538-597) in China, it was believed that we were about to enter the final Dharma age, "Mappo". Capacity is so degraded in Mappo that the only way people can reache enlightenment is directly from the Eternal Buddha Shakyamuni.
The Tendai shu and Nichiren in his early career believed that Buddhist practice was only for a few talented people. They used all kinds of complicated Esoteric practices not suited for everyday use by the common folk. It was on that point that Nichiren evetually broke away and developed a practice so simple and elegant that everyone, Monk and commoner alike could practice it. It was also so potent that a devoted person could reach enlightenment in his current body.
The formula was thus. The Lotus Sutra is the Buddha's highest teaching. It contains the entirety of his enlightenment. The entire Sutra and all of it's merits is contained in it's title "Myoho Renge Kyo".. The Buddha's Dharma ( his word) and the Buddha are identical. Therefore if one hears the Title of the Sutra ( by chanting it) with faith ( adding " Namu" or "devotion to". Thus making the entire recitation "Namu Myoho Renge Kyo") you had the complete practice.
When one takes in the entire Dharma by hearing it, the seed of enlightenment is thereby planted within your life. After awhile one takes notice like a pregnant women who does not at first feel her child but later becomes aware of him ( Paraphrase of Nichiren). Nichiren belived that you thus commune with the Buddha who actually indwells within you, transforms you and leads you to enlightenment which you cannot ( In Mappo) reach by your own power.
The Buddha actually exists as a Divine Supreme Being who has eternal life.
All people have the ability to become enlightend, not just a seperate class of Monks
The Word ( The Sutra) and the Person are for all intents and purposes identical in merit.
You achieve enlightenment by communion with this Supreme Being and by his grace alone.
You commune by hearing the Dharma encapsulated in an easy to use form, the Title of the Hokkeyo .
The Buddha thereby indwells within your life and transforms you..
Sound at all familiar ?... Nichiren was a smart cookie. He got an awful lot right.
( Yes, it was the Mongol invasion)