UU always had little problems, that didn't seem like a big deal but quickly caught up with them. The whole seeling point of the UU was that it was a new universe, without confusing coniunity issues, but that is no longer the case after 9 years. So their main selling point is gone and the little problems have begun to pile up. They tried to burn through 20 years of 616 stories in 6 years, everything felt rushed, almost every storyline felt rushed characters were introduced to the UU with no thought and were extremely underdeveloped (ex: does Sandman or Eelctro have any personality to speak of, when is the last time we have even seen Sandman?) Add to that the big problems created by Kirkmana nd Loeb and you have a tempus in a tea pot.
At this point I think the new Spidey cartoon is a better retelling then USM, they have given almost every character introduced a personality, maange to baalnce the A and B plots nicely and haven't killed off caracters for shock value. The animated versions of Sandman, Vulture and Electro are vastly superior to Ultimate counterparts.