No, the cons were minimal. The good far outweighed the bad.

Ultimatum's story was executed poorly, this much is a given. But Ultimatum as a concept was absolutely successful. It forced the Ultimate Universe as a product line to be a different and unique beast from its parent line.

For far too long books like X-Men and Ultimate X-Men were far too similar thematically and tonally. It unfortunately has to do with the original success of the Ultimate line of books influencing the other all too well. The Ultimate line became redundant immediately after the mainstream product line incorporated a lot of what the Ultimate line so successful. With the two lines so similar, it was either give up on the now struggling Ultimate line or attempt to salvage it.

Ultimatum was that attempt to salvage things. And it worked for a good time. Ultimate X-Men took off again. The Ultimates improved. And Ultimate Spider-Man chugged along respectably as it always had. The line was saved via a poorly executed story that forced the line to abandon old characters and stories and themes for all-new ones. The X-Men were reduced to a small group fighting not for peace and integration but survival, and it was a fight that they almost didn't win (in a story world where anyone can die, that threat was legitimate). The Fantastic Four were gone and Reed became one of the greatest villains Marvel has ever published. And...Spider-Man kept chugging along.

It was one bad story that served a much greater purpose. Yes, it could have been executed better, but the ends really do justify the means in this case. We had a line that was so much better coming out of the event than going in. It didn't last, of course. But there's only so many things you can do to right a sinking ship.