To everybody being negative that we're getting the Ultimate Fantastic Four's origin, Fox used Ultimate William Stryker before and that worked out okay and even Marvel Studios have used versions of Nick Fury and Thor that owe more to Ultimate than 616 to say nothing of the Chitauri appearing and comments that Aaron Taylor Johnston was to research Ultimate quicksilver for Age of Ultron.
Fact is, Ultimate did a lot right. The whole Donald Blake Thor thing was confusing to new readers and Ultimate Thor was a lot more streamlined. Nick Fury and Black Widow both having the Infinity Formula was contrived. Having Fury not have served in World War 2 makes a lot of sense and it also means that Black Widow feels a whole lot more special if she's the only character who took the Infinity formula.
And it's telling that the mainstream Marvel U is going to change in September to be combined with the characters and elements of the Ultimate U that worked. Ultimate Gwen was already teased.
That's not to say that there aren't things I disliked about Ultimate. I really dislike Ultimate Cable and Scorpion, I'm not a fan of Quicksilver and Scarlet Witch's relationship either. The previous Fantastic Four suffered from using Ultimate Galactus instead of 616 since that wasn't a version of Galactus that I've ever been a fan of. But on the whole, Ultimate brought in a lot of really cool elements that I'd like to see in the 616 universe.
I can also do with some changes like Heinrich Zemo dying in the war and Helmut being his grandson instead of son, Cable and X-Man becoming one character, a chance for Jean Grey to return with a backstory that's far less confusing, opportunities to make characters who I've long despised like Triathalon and Feral cool, New Universe characters being rebooted in the mainstream U, etc which have nothing to do with Ultimate but would still be cool to have in a reboot.