Since the Beyonder is from his own private universe (not to be confused with his own private Idaho), why not use the same Beyonder, just have him happen upon the UU and think "hey, re-do!". This time, however, there is no Molecule Man to foil his master plan.
Maybe not... but I like the idea. SWI and II were pretty awesome back in the 80's, everyone I know who collected back then had most of the issues from both of those minis. I just hope the Beyonder would modernize his wardrobe for the Ultimate Universe. That flared collar is very tacky by today's standards. Oh, what, some people would rather see the more recent "Secret War" style from 616? Why? That was horrible.
If it happens, I'd love to see it start off in UFF, since Reed is always finding all of these new Universes. He may be a little hesitant right now, after the zombie universe scare, but the Beyonder's universe was like a blank page in 616... he might see something like that and visualize a big opportunity, study the blank universe, only to be followed back to the UU by the Beyonder... and that's what starts it off.
Of course, as I said before, it could always be the same Beyonder from 616 but with a different, more educated plan since I'm sure he learned a little humility from his defeat in his previous endeavors.