I really liked the Ultimate Universe. I thought it was clever to run two universes, re-building the characters in the Marvel Universe and giving a fresh start, without sacrificing their main universe.
For some reason, the ability to kill characters seemed more important than actually having compelling stories. Why kill off Peter Parker? I quite liked that title.
The Fantastic Four was quite different than the main universe title, with Reed going a little bonkers.
The whole "Reed and Sue" have to have a kid prospect was weak. Particularly given that is not what happened at the end of the story. Was it really a 50/50 split to see if it was "Sue"'s kid or "Reed's" kid that made the difference in keeping all of reality going? I guess it would be less that 50/50 'cause it was presented as the offspring of the two of them.
The "resolution" that Sue didn't forcibly extract "genetic material" from Reed was nice, though stealing some of Ben's does not make Sue a very likable character. They did help make Reed look less evil, and maybe recoverable, but not sure why Sue (who seems to love Ben and vice-versa) would steal his "material" without consultation or discussion (or even create a child the old-fashioned way). If they really felt the "Reed-Sue" child was not an accurate requirement to offset Galactus (or the swarm), they why the sneaking around?
I'm not sure where Marvel is headed, but it seems downward. I know it is difficult to keep characters running for 50 years, but the new model of very strange story-lines dramatically changing characters seems self-defeating and short-term.