My concern about the merging of the two Universes is how much of the "dark and gritty Wasp-eating, drug addict mutants, jerks-in-costumes Ultimates" aspects are going to get ported over.
Well, Mark Millar seems to be not working for Marvel anymore, so a lot of those tendencies have gone away. Kyle and Yost still get work sometimes for them, so there is still is cause for concern.
The last two years have seen a pretty tame UU in terms of jackassery and lethality. I'd say they already took a little part of the over-the-top grittyness and a lot of the moral ambiguity and made it part of the 616 universe with their big storylines since Civil War, which is why the UU is pretty obsolete nowadays.
I think they won't do a full reboot. They are mostly going to finish the UU and situate some of the more interesting characters in the core 616 universe. I am crossing my fingers that Ultimate Peter Parker and his supporting cast will make it, but since Bendis will want to place his golden child, Miles Morales, firmly in the 616 universe, I sadly doubt it.
What really pisses me off is that apparently the rest of the multiverse also got killed off in the collateral of this big storyline.