Hm. I actually like Other M. I suppose you're a fan of the Prime games? I am not. They ruined the series, as far as I'm concerned. They took away Samus' agility and made Samus into a troop completing objectives like it's Halo or something. I know, Other M had you taking orders, but Other M was created by one of the co-creators of the series whereas the Prime games were made by Americans overseen by Miyamoto who had never worked on a Metroid game before. By no means am I saying that Other M was flawless, but I greatly appreciated Other M's authenticity, especially as far as gameplay goes.
So, yeah. As far as I'm concerned the Prime games didn't happen and I've been perfectly content with the lack of Prime references in the previous Smash games.
As far as my least favorite aspect of Smash 4, I'm going to agree with some others here and say the Miis not being playable online. I believe Sakurai made a comment about how he didn't want the online to be a copyright free-for-all, but Miis are playable online in Mario Kart 8 so I don't see what the problem is. I recall there being several "Hitler" Miis online in Mario Kart Wii. I think if we can handle that then we can handle Ice-T or whoever else they make.
I think there was also a comment about not wanting the characters to have unpredictable moves online, which is also why custom moves aren't allowed online, but honestly, I wouldn't have any problem with custom moves in online matches. The variety might actually make it less stale. But, whatever...