If you remember, though, there was a mention of The Ultimates in the first arc as well and they weren't meant to be formed until after Fury took over after Ross' death.
I think that the first arc was being written as taking place in the past, but then Marvel decided they wanted to make it happen in present day with the rest of the titles. It's the only explanation that fits, really. Quesada (I think) had said that Ross' appearance in the first arc was a mistake, but neother Bendis (who wrote it) or Millar (who plotted it) are stupid enough to miss that. Clearly, they fully intended the story to take place back when Ross was alive (which would explain other mentions of them in Spidey and Ultimates), but things changed and Bendis had to insert that mention of The Ultimates in #5 (or 4, whatever) to set the scene as present day.
Now, Ellis explains (sort of) that Ross survived the attempt on his life by Weapon X, which helps continuity, if only a little, rather than hurting it.
I argued that exact point at first, Goody, and nobody agreed with me then. Now, I change my view of it, and you agree with my original idea. Figures...
It doesn't really matter now, though. UFF is set in present with the rest of the titles, and Ross is officially alive. Despite this conflicting with previous mentions and appearances of the FF, there's no need to create further problems by complicating things any further with Ross. He's alive, so why play around with the timeline?
I think the timeline stands as current. There have been so many errors in UXM and USM, not to mention the Team-up series, that I barely count those as ultimate books. It seems as though (through the 616 too) that a writer decides to kill off a character without consulting anyone at marvel as to whether it's a good idea or not. You can't just go around killing important figures like ross without some serious justification, especially in such a young series and the character hasn't been fully explored yet.
Also I wish they could just have a little board in the marvel offices marking which characters are currently in play, and who is where in the world so that they can have some decent cross continuity. I know it's probably only a gripe, but with Nick Fury currently in russia, and sorting out the hulk trial it feels uncomfortable. Of course the ultimate nightmare thing would have to have happened some time ago. But it mahr-vehl joins the team, then he will have to appear in the regular ultimates comic at some point. along with falcon. So these things should really be carefully planned.
But perhaps that is just me being too picky.
Oh, but a nice piece of continuity was reed developing the new 'spaceship' in UFF, for it to get played in Ultimate Secret.