I think there's a valid basis for comparing Ultimatum and Countdown, as they're both (in the eyes of fans and critics) rather outlandish failures. Countdown didn't do anything to lead into Final Crisis or bring secondary characters into the spotlight. And Ultimatum, I think, will prove to be a failure as it attempts to reboot the Ultimate U continuity.
Still, I think Ultimatum is the "worse" title, simply because we can more easily ignore Countdown. Speaking for myself, Ultimatum completely ruined most of the line for me. The wholesale slaughter of most of the interesting X-Men keeps me from developing interest in that book again. Killing off Janet and Thor removes two of the more likable characters from the Ultimates. Doom is gone, so that removes impetus from the Fantastic Four. And some of the survivors (The Thing, and Quicksilver) were painfully OOC by the end, and I'm going to have a hard time being able to enjoy them after all this. And all this isn't even touching on the level of violence porn throughout the comic.
I guess the saving grace in all this is that Ultimate Spider-Man's cast seems like it'll remain mostly untouched (aside from a nice character arc for Jonah Jameson). Because, really, what about that book *needed* a reboot?