It's fashionable among some people in a fandom to bash the current big thing. While there are many justified gripes with Awakening and Fates there are always a select few who hate them out of spite because they're popular. Then you have the tiny but very vocal minority who feel threatened by the huge wave of new fans because their niche fan base no longer feels like an exclusive club house.
I'm in the Doctor Who fandom, which is VERY familiar to this one. You have the old school fans who grew up with the classic era, the new fans who first got into the series because of the Tenth Doctor, the classic elitists, the new fans who complain about elitists, etc. When you have a series that has gone on for so long (whether it's a TV show or video game) it's inevitable that the fan base will clash and get extremely divided.
Honestly I have yet to meet anyone who only liked the series for the avatar system or "waifus." The only time I ever hear the term "Waifu Emblem" being used in a serious manner is when Awakening/Fates detractors (I dislike using the term hater) bring it up. It's a cheap, easy stock argument some of the extremely vocal hard core veterans fall back on. They invent an imaginary scapegoat. It seems Echoes gets less hate because some of those dissatisfied with Awakening/Fates see it as a return to form despite the game being just as guilty of committing the same crimes (bland maps, one note characters, and yes there is still blatant fan service. Also Kozaki doesn't do the armor designs.)