I feel that if Millar had written Ultimatum, it would have been a conclusion to all his work in the Ultimate Universe. We would have had Magneto executing his ultimate plan (remember when Magneto said he was going to try something new at the end of BKV's Magnetic North? He should be doing something new!), the truth behind Jean Grey/Phoenix, Xavier's real motive, the connection between Namor and the Inhumans (I remember reading this in one of the solicits and we never saw it - I always presumed that Attilan and Atlantis were enemies so maybe in Ultimatum we would have Namor declare war on the Inhumans on the moon), Doom escaping the Zombie Universe (I can't believe we haven't seen this yet - this scene writes itself!), the result of the Ultimates/SHIELD split with Pym as the new prisoner in the Triskelion, exploring more of the new Banner/Hulk dynamic, Fury/Hawkeye exploring the people funding the Liberators - introducing HYDRA and the secret war SHIELD has been fighting for years, Thor's true purpose and the exploration of Ultimate Asgard and of course, the genetic war - human vs mutant vs superhuman, which is what the UU has been leading to since it begun - and it all revolves around Captain America's super soldier serum. And Gah Lak Tus would fit in there somewhere (I believe Millar was originally going to write the series but didn't have time).
Yeah. Obviously that's a bit of a mess and the ideas would be better in their respective series but I think if Millar had written Ultimatum instead of Loeb, it would have been a hell of a lot better and would probably make a lot more sense.