I Say we should give it a rest, suspend some disbelief, and pretend that Iron Man did not mention the Fantastic Four in Ultimates #2, and that They didn't appear in the USP Super Special.
Thats two things right there. They have plenty of ways they can (and probably will) explain the General Ross switching from Head of SHIELD to the Head of the Baxter Building. Plus, Dr. Doom has never been mentioned as the leader of Latveria, Latveria is a screwed up place w/o doubt, but there is nothing other than one portrait that defines him as the Leader, so lets just say he's not yet. And Some things in UMTU -are- important. The Introduction of Daredevil, and his character's dislike of Peter. Wolverine meeting Spiderman, then the X-men meeting spiderman (hell, its even important that Sabretooth is working for the government, that was before his appearance in the Weapon X arc). It has Fury recruiting Black Widow. It has the introduction of Curt Conners and the Lizard.
And someone brought up if 616 Continuity is this badly screwed up?! How about Magneto ripping apart New York City, and No one, in ANY other Title (despite how many of them take place there, especially Spiderman!) Notices! And then After Magneto kills Jean (again), Jean speeds off to a future where Everyone is Pheonix! Then claremont comes back, and all of a sudden, the guy who was there before Wasn't Magneto, and Magneto is magically the same guy with the same personality Claremont left when he left the comic, and back to being best buddies with the Prof.
Then how about rebooting the Spiderman storyline so that Aunt May could come back to life after dying after a long hard bout with some disease, and now modern comics reaching back to Gwen Stacy's death, which was simplified out of this reboot. In the Spiderman Continuity that Gwen Stacy died, Aunt may died. And now its the two right on top of each other. Plus Dr. Octopus is alive/dead too.... and god. I dare someone to try and explain the horrifying complexity of the Clone Wars....
Hmm... oh, and Now, back to X-men. In Astonishing X-men, they're meeting up with the Fantastic Four, who never recalled the Baxter building along with everything else getting ripped up by the Not-Magneto fellow. And with the Pheonix Endsong Miniseries, Jean grey's spirit is absorbed by the pheonix from her dead body, when we know that her mind is billions of years in the future....
In Ultimate Marvel we have possibly around 10 continuity problems, in 616, we have hundreds upon hundreds. DC is a lot better than Marvel with continuity, but there everyone complains about the complexity they go through to make things work out all fine and dandy.
I Have no problem with the few problems in the UU, and trust they will get addressed. If they dont get addressed, I might have a slight objection, but i'll still enjoy the books as much as I do now.