Let me put it to you this way. In Ultimate Marvel Vs. Capcom 3 it is being hinted that Megaman X is going to be Zero's alternate costume. Fans have begged and pleaded for X to be a playable character, but Capcom did not include him into the game. Tell me how this is going to play out with the fans? I can give you a hint, it starts with "outrage" and ends with "disgust".
The same thing will happen with Super Smash Bros. 4. There will be countless threads whining about how character "x" is only a mediocre costume and not a full character. On top of that it is a hollow consolation as underneath nothing erases the fact that it is just Samus with a Dark Samus skin. So it isn't even all that satisfying, it is like eating a tofu burger when you really want a Whopper. It doesn't do it.
Good way to put it. But I think that would really only happen with popular characters.
Besides this is Nintendo not Capcom. Nintendo handles thing way differently then Capcom, Capcom fanboys know Capcom is aware of their opinions, hense: DLC, polls, suggestion box.
Not to mention that MM had much more popularity to get into MvC3 then any of the other characters who could get into Smash now. In addition, with how Capcom has been dealing with MM recently, of course people are going to think it's trolling.
Zero had a MMX style costume in the original, but did people freak out then? No. It was after the all the MM cancelations, then people started to really care.
In addition, Capcom has recently been doing character costume blogs for each character in UMvC3. Have people been freaking out about that? No.
I can understand alternate costumes hatred, but costume colors inspired by other characters is nothing to freak out about.