I'm not sure Fire Emblem's choice can be seen as the attempt to revolutionize the choice system in videogame narrative, but more like a really good way to capitalize onto two (three?) different game versions; hence the flaws that are underlying become the product of a monetary -not narrative- focus. I sure get your point as to why it could be disappointing, but really, you should have seen this coming from the start, as I'm not sure at any point the developer was trying to really make you feel a meaningful plot point rather than the justification to chop the game in three different parts. Mind you, I haven't played the games, though, so my opinion here might not really reflect how truly goes within it, but that's the impression I've always had and your critique kinda confirms it.
Lack of impactful choices, despite the media hyping them up, is nothing really new. You already pointed out Mass Effect 3 example, which we were promised something along the lines of "there will be tons of endings based upon what you've made" that ended up being "choose your favourite colour"; unlike Fates, though, I think ME3's problem was a lack of time to properly deliver on this end rather than, as I said earlier, a plot point made purely for monetization. You also talked about Telltale's games as meaningful choices, but this is rarely the case on the long run (static endings, at least in the case of The Walking Dead 1 and The Wolf Among Us), for some reason, their consequence system ends up losing steam in the final moments, and I'm pretty sure most people got the same ending in both games regardless of the diverse amount of choices they had to make beforehand.
The way you described Fates' lack of impact when it came to actually make the decision reminded me of Wolfenstein: The New Order. A great game, but one that suffers from the same thing: you have to make a choice very early on, one that supposedly changes the whole timeline of your game, but at that point you haven't been invested enough to really feel any weight in the choice you make.
