Pretty much the only thing people can point to.(And even then,a 616 version would've been just as good)
SHIELD bringing The Avengers together is pretty narratively useful.
As is tying The Hulk into the attempts to recreate the SSS, as well as being less silly sounding than the nuclear bomb thing.
I thought the Ultimate version of Dr. Doom was perfectly fine, and his first storyline as the villain was pretty entertaining. I think the complaints about that version "ruining" the character are silly.
Sue Storm being a biologist instead of just "Reed's girlfriend" is a vast improvement on the mythos.
Captain America's costume from Ultimates2 looked great.
Making Captain America overtly superhuman is a vast improvement over that pointlessly vague and pedantic "peak human" nonsense.
Most of Ultimate Spider-Man was pretty good. I thought the issue where we saw things from Norman Osborn's perspective was great, and I found the post-Ultimatum retool of the book into a sort of team book with Kitty Pryde, Johnny Storm, and Bobby Drake joining the cast was thoroughly entertaining.
The penultimate issue of Ultimates2, with the huge battle in DC and Tony Stark piloting a giant space warship and all of those mechs and Captain America and The Colonel having a lightsaber duel along the National Mall was just plain fun.
The whole "most of the characters don't actually believe that Thor is really Thor" thing and his having this kind of pagan messianic status, while not perfectly executed most of the time, is a pretty cool take on the character.
I found Mark Millar's run on Ultimate Fantastic Four to be really fun, albeit in a schlocky pulpy kind of way. Not a whole lot of deep thought going on there, but I had fun reading them, and there's nothing about those issues that I'd really call bad.
I thought that Ultimate Red Skull was a neat idea for a character.
I think making the Ultimate FF collectively younger was fine. Not an improvement, but it wasn't worse either.
I really like the idea from Ultimate X-Men of mutants using superhero-esque code names being a way of establishing a subcultural identity for themselves separately from the mainstream human culture that rejected them, instead of just being an extension of the superhero genre conventions. That's a really cool idea that adds a lot of texture to the mythos.
In general, they had a few really good costume redesigns.
Bryan Hitch is a great artist.
As is Mark Bagley.
As are the Kuberts.
That's probably about it. There's plenty about the Ultimate line that wasn't so good, but there are definitely some good ideas there worth mining for the films, as the films have been doing pretty consistently since day one. As long as you selectively pick the good stuff over the bad stuff, you're fine.