I'm not sure if that's been a big deal for Fire Emblem. I've read that even some older fans like the new stuff, though you can take that for what you will. I mean, besides the fan service (which really isn't that big of deal when you actually play the games, or in my case, Awakening since I haven't played Fates yet since my sibling has it) and the over powered pair up mechanic, Awakening and Fates still retain their core gameplay that has evolved from previous entries of the franchise. The weapons triangle, the free roaming overworld map, permadeath, the change of classes, character tropes, special skills, etc. are all in the recent games. And while the waifu thing is prominent in the recent games (which I don't really think is a problem, personally), its not like the support and marriage system isn't new. Its roots were back in Geneology. It also helped that casual mode became a thing back in FE12 (Mystery of the Emblem remake) and was applied in these games to allow new players to play since permadeath can be a factor for new players due to fear of losing units, especially early in the games. So ultimately, the recent games of Fire Emblem didn't really go through that much of an overhaul, they just combined everything from previous games, utilized new art, and allowed the game to be more accessible. You could probably argue the three paths for Fates being new in the series, but I'm not sure if that is considered a big overhaul.

As for Metroid, I would argue it kinda went through that kind of particular treatment with Other M, maybe a little more than Awakening or Fates. Mainly trying to go for a more story focused game with Samus having an actual voice, more focus on her relationship with some of her peers and issues with her past, and mix 3D Prime and 2D traditional Metroid. Unfortunately it didn't pan out due to some problems here and there, mainly the story and characterization of Samus.