Short history lesson on State Shinto and 'officialdom':

Yes and no. Part of the problem is that there is no one true Shinto orthodoxy. Granted, from the Meiji Revolution to 1945, State Shinto was considered the 'official' Shinto, and dictated which Kami were to be venerated and how. Initially this was a political move - Meiji felt that the Buddhist temples across Japan had enough economic and political clout to challenge his absolute rule, and went to great lengths to force a separation of Buddhist and Shinto practices (which had grown together into essentially one religious unit, over the past 1000 years. The only ones left relatively alone were the 22 Shrine-Temple complexes authorized by the government to remain 'as is', such as Mt. Hiei, Ise Shrine, et cetera.

Meiji's efforts weren't anything new, per se. In earlier times, the Jingikan ("Office of Heaven on Earth") regulated official views on shrines, offerings, and the like. Due to Shinto's extremely local practices, however, these regulations never approached the level of an orthodoxy. Nobody ever went out and said "Your Kami aren't real Kami. Worship these instead." At least not with any sort of official clout, they didn't. They sometimes said, "Your Kami are also called X, in Heiankyo, Y in Nara, and Z in Bumpkinville, in Sado Province."

What this means factually is that there are tons of nature Kami, from the big and important that everyone knows about, like Susanoo, head Kami of tricksters, lord of the oceans, freaker-outer of celestial weavers, and subduer of eight-headed serpent beasties; to the ones that have regional providence, like Takemikazuchi, "He Who Speaks Thunder", master of Namazu-the-catfish-of-earthquakes; to the extremely local, such as the Kami Of That Rock Over There. Certainly Shinto is highly animistic in nature, but Kami are not entirely - or even in majority - spirits of nature in the way the Native Americans had them, or how we think of them today. Many Kami have dominion over a thing because it's their job, not because it's what they are. To get it to rain, one wouldn't generally make offerings to The Big Bad Kami of Rainstorms, as one might imagine (Taki Tsu Hiko), but might make offerings to the local weather controlling Kami, "Taeko-Hime", who was once a young girl from that village who did something really cool and was taken to be both divine and historical.

Basically, Kami come in three flavors:
1) 'First Wave' or 'Epic' (aka "Kotoamatsukami") - those contained in the Nihon Shoki and Kojiki, said to have come into existence with the rest of the universe, such as Ame-no-Uzume, Susanoo, and Amaterasu - who is not, as it's usually thought, Kami of the Sun. She's 'Kami of Divine Solar Radiance.' I keep meaning to make her as a Zenith Caste Solar Exalted, but I never get around to it. These Kami are known all over Japan, have equal influence everywhere, or are otherwise taken to be extremely powerful.
2) 'Legendary' - Ones that are regionally prominent, but probably occasionally venerated elsewhere. Examples are Takemikazuchi, the Kami of the Gion matsuri (technically not a 'pure' Kami, but a gongen - combined Kami and Boddhisattva), or the Kami of Iwata City, whose name escapes me. Well known, but not universal.
3) Way local Kami. Kami like the Gate Guardian of Itsukushima Shrine, the Kami of Bob's Prize Fig Tree, the Kami of That Funny Rock Over There, or the Kami of Frank's Grandma. Most ancestor kami (ujikami) are in this rank unless they did something really spectacular, and then they tend to be pretty damn famous. Like, say, Hachiman. Or Emperor Jimmu.

These amount to a subtle difference from totemic or shamanic spirits like Sun, Sky, Praire, et cetera, but an important one. Especially given the fact that Shinto methodology is much more hermetic than shamanic. Those rituals are extremely precise, relying on highly codified formulae.

What does this teach us? 3 things.
1) If you don't like what Shadows of Asia said about a culture's practices, learn it for your own damn self and make your own conclusions.
2) If you get me started on this subject, I can and will talk your ear off about it.
3) Do not let your children gun for PhDs. The above post is the result of that happening.

If Shadowrun Catholicism had quit worshiping God and just worshiped the saints, changed the title of priests to nuns, and declared nuns were usually, but not always female and provided no explanation of any kind would you use the words ‘fictional license’ to justify those changes?

This is clearly poor research, or more likely no research at all, otherwise there would have been some notation of how the ancient religion of Shinto had changed completely in so many ways for no apparent reason. Or at least a mention that it had changed.

It would require more than a sentence to have hit the cutting room floor, it would require several paragraphs which also need to describe the removing of all traditional Shinto priests, the upgrading of shrine maidens to priests, the removal of all the kami from Amaterasu to the kami of That Rock Over There as objects of worship, the veneration of ancestors going from a small family affair to a public veneration, and the reasons that all these ancient practices would be so radically changed in such a short timespan. A bit on how the changes were managed on something so decentralized as Shinto would also be helpful.

I wish Adareal had written the section on Shinto, as he or she clearly knows something about the subject. Whoever wrote the SOE 'Shinto' section clearly didn't even spend five minutes with a websearch program.