They probably will, but at the moment its just making for an annoying scene of Foggy yelling at Matt without telling us why.
Actually, Bullseye is alive (I think, unless he was killed off during the recent Elektra run), as is Kingpin (I think; he might have been killed during Secret Wars, but it seems all the deaths from that have been wiped), while the Hand just showed up in the last issue to take revenge against a guy who stole some of their power. He's got a few other villains, but they're also up for creating new ones.
Scott never really turned evil on panel. Rather, he became more anti-heroic thanks to PTSD that never got treated, and after losing all that was left of his family while mutants as a whole were left near extinction. He did do some morally questionable things, but was doing so for firmly good reasons (and against people who deserved it), and weren't any different than things done by Xavier, Beast, Nick Fury, or Steve Rogers (hell, he's probably responsible for less death than Steve is, given what happened in Warren Ellis' Secret Avengers run).
The only reason he's 'evil' now is because people keep saying he is, despite the fact that he's not done anything new. Hell, he only killed Xavier because he was possessed by a corrupted Phoenix and Xavier was attacking him; he's only responsible for Xavier's death as far as any superhero possessed/mind controlled is. Its actually really hypocritical in some cases given Wolverine was the most vocal about it, despite the fact he killed Northstar a few years ago under demonic possession, and while Scott went out of his way to fix the damage done during AvX, Logan and Steve have denied responsibility for it despite being just as responsible.
In fairness, the Ultimate Universe had become a mess. Besides Miles, no other book was able to stay afloat and were lagging in sales because it was so hard to get new people into the continuity of it; Miles is easy enough to explain to new readers, but trying to explain the All-New Ultimates or Ultimate FF would be a nightmare to a new reader (not helped by the fact Ultimate FF was super skeevy and gross). Apparently a few others have made the jump besides Miles at least; Maker is bothering the New Avengers right now and Boombshell is somewhere, but not sure where.
In all honestly, besides a few points, I actually like the current comics. They're different, but at least they're creative, and some of the new ideas I quite like (Kitty and Star-Lord were surprisingly endearing as a couple, Sam-as-Cap is the closest thing to a Falcon ongoing, New Avengers is probably one of the best Avengers relaunches ever, and a number of other books are great). Besides the above, my only issues are with Spider-Man (sure, show us a great alt where Pete and MJ are married with a kid, then tear it away with Spider-Man as Batman Lite), and Hawkeye (Lemire's characterization of Clint and Kate seems to be like a bad fanfic of Fraction's run that exaggerates the worst aspects and leaves out the endearing parts). And the lack of a Young Avengers book, but I'm making do for now by planning out my own fanfic for that.
(Also, sorry for the super-long reply)