Speaking of how Link's Awakening looks. Not only does it have REALLY if not perfectly similar artstyle as the artstyle used to portray the Mother cast in Smash, it's also a remake of a very, VERY old game that I'm sure not many people have played or expected to see, specially the newer generation.
This is no solid reason, but I once talked about how I could see Nintendo remaking Mother 1, 2 and 3 to introduce it to the audience that likes cute games like Animal Crossing and/or RPG's like Bowser's Inside Story.
Since Nintendo decided to remake Link's Awakening and introduce it to both old and new gamers, I could see them wanting to make a remake a cute, more colorful RPG like Mother for those audiences, instead of expecting them to purchase a serious anime SRPG like FE (No offense of FE, I like FE. In fact, my favorite is Awakening).
This would mean we would not get a Mother trilogy or a Mother 3 localization right away, since it would be impossible to expect 3 fricking games announced together and in 3D. But we would get to see Mother 1 in 3D and completely improved, with the potential to use the engine and assets to create Mother 2 and 3 in the future.
Wouldn't be hard to believe considering we how they keep making New Super Mario Bros games, despite not being new anymore, or them using the same Engine from the Ocarina of Time remake on the 3Ds to make a Majora's Mask remake. Or how they used the same console and engine to make 2 gens of Pokemon in the same console... twice (gen 4 and 5 with the Ds and gen 6 and 7 with the 3Ds).
And hey, if they remade Mother 1, I could see them putting a bit more of story, cutscenes and content. Maybe add the battle mechanics that Mother 2 and 3 have. (And yes, this means that we would also get our boy in a redesign)
So yeah, my point is that, if they decided to bring an old game and remake it to introduce it to both old and new audiences then I don't see it as much of a stretch to them wanting to do the same for Mother in the future, it's not like Itoi doesn't want Nintendo to use his characters or anything. He's much more willing to let Nintendo use his characters than Game Freak was with the Smash Pokemon amiibos in Mario Maker, which didn't have their cries or victory themes.