Wouldn't this kill Mii Costume Theory as this implies that there won't be a lot of costumes from Square Enix?
No, that wouldn't.
Mii Costume Theory is that costumes from the respective companies of the characters being focused on would be revealed in the character specific Direct. Thereby, as the theory suggests, the Hero would be accompanied by Mii Fighter costumes from stuff like Final Fantasy, Dragon Quest, The World Ends with You, Super Mario RPG, and others.
The scenario that would rid us of the Mii Costume Theory is if Namco or Capcom costumes are revealed alongside Square Enix content, or with Microsoft content in Banjo-Kazooie's mini-Direct. Or at least, that's my take on Mii Costume Theory. The overall amount of costumes means nothing toward the Mii Costume Theory: it's what gets revealed and
when.
Basically, the idea (which really isn't all that farfetched if you ask me) is that costumes related to the company of the revealed character are what would be revealed. The only precedent to go off of is Joker and Atlus/SEGA (because SEGA owns Atlus), but the bigger thing is if that precedent continues or doesn't.
So something like:
Hero Direct- Geno, Chocobo Hat, Sephiroth, etc
Banjo Kazooie- Mumbo Jumbo, Gruntilda, Jinjo, Master Chief, Joanna Dark, etc
Obviously it's entirely possible that costumes for different companies would be revealed in these Directs, for example Lloyd Irving and Heihachi in the Hero mini-Direct. I'm not saying that can't happen. It just comes down to what happens in the Hero and Banjo mini-Directs.
I happen to think it's possible that Capcom and Namco
do get the final two characters. But by no means is that set in stone.