I don't play Fire Emblem anymore, I don't buy new Fire Emblem games, so honestly this doesn't really affect me directly in any way. But if it were a series I actually cared about, at this point I think I would be at least a little concerned. Direct censorship is always bad, even if it is done for the "right" reasons. I don't think it really matters who is doing the censorship either, although that can cause more or less distress depending on the process. When Spielberg alters ET for the re-release, it is stupid. When Lucas decides to change the context of scenes when re-releasing Star Wars, it is stupid. When studios decide to censor movies to release them at lower ratings in cinemas, it is annoying. When studios decide to censor movies for foreign sensitivities to reach a larger audience, it is annoying.
In many cases, an argument can always be made for why changes are made. But that doesn't change the fact that it is annoying that works cannot stand on their own for what they are. That's not to say that every piece of work some amazing work of art worthy of eternal preservation, but rather that I think each piece of work should be allowed to stand for itself to be judged by the audience.
I don't want to play a SRPG with casual homophobic stuff, or creepy face rubbing minigames where you get "closer" to your party members. But I think I still wouldn't want to play such a SRPG even if such content is removed from a single version of the game. If Nintendo of America truly feels that such content is offensive and should not be in their games, and if they truly feel that the content in FE Fates could be classified as such, then they should have been to reject the game for localization. Of course we know this is not the case. This is a business and marketing decision meant to distance the brand outside of Japan from Idea Factory games. I think we can all accept that, because business is business, but I'm not sure if championing or celebrating that decision is in the best interest of consumers.
If the next Fire Emblem game in Japan doubles down on this sort of thing, is the English fanbase going to essentially turn into one that encourages and demands for continued censorship in every game just so they can pretend to feel better about a series that they would otherwise feel weird about liking in the original form? That would be so weird to me.