Number one: Get Bendis and Bagley out of the UU until he can come up with some original ideas that don't make it look like he's rushing through the planning stages and half-assing it all the way to the bank. There are so many glaring examples of his Shenanigans in USM that it makes one's head spin. The Clone Saga did NOT need to be redone. When the original clone saga happened in the 90's, I dropped all my subscriptions to Spider-Man titles. It was too convoluted then, and it's too convoluted now. Bendis COULD HAVE improved upon the concept but he failed. MJ as She-Wolf and Scorpion being nothing more than a Parker clone were horrible. MJ should always be without powers (see Strangefate's post) and Scorpion was/is a major player in the Spider-Man mythos. In the UU, he's no more than a Parker clone destined for obscurity and/or a quick death. Other examples of Bendis' incompetency at making old things new or making new things awesome: Deadpool and Omega Red having any part in USM when it's a no-brainer that they should've ben introduced in UXM or a UXM-related title (such as a Wolverine mini or the like), Ultimate Punisher (what a horrible, horrible Ultimization.), Ultimate Daredevil being a total a-hole, Ultimate Morbius looking like he came straight out of a 70's book. The list goes on, but I'd like to move on from Bendis and the total decline of USM.
UFF is good, but I would like to see more consistency between writers and artists. There seems to be a change in looks and attitudes and situations when the creative staff on this book changes. I loved Millar's run, and I liked Ellis' run (except for the Doom with goat legs crap) and I'm enjoying the current arc. However, when the staff changes, it's like we get a whole new version of the UFF. I don't like that very much. Also, it's time to put a cap on Reed's genius. We don't have to stop him, but the whole idea of him getting smarter and smarter as every second goes by is stupid. If that was the case, there would be no need for the Ultimate Universe because he would've cured all diseases, stopped all crime and invented safeguards for earth to prevent alien invasion. He also would've built a better mousetrap, broken the tax code, been able to provide food for every hungry mouth on earth and stop global warming.
Ultimates. I have no complaints! Oh wait... yeah I do. It would be nice if Ultimates came out at least every TWO months as opposed to every FOUR months, and I would've liked to have seen some of the villains that Millar and Hitch introduced stick around a little longer. Still, I can't complain about that because the way they've all died has been light years better than anything they would've done had they lived. Abomination getting his lunch eaten by the Hulk, Hurricane getting liquified by Quicksilver, and Dynamo getting vaporized by Iron Man 6... BRILLIANT! All that being said, I am not looking forward to Loeb and Mad's run on the Ultimates. There is no way in hell it can stand up to the last 2 volumes. Millar and Hitch are a hard act to follow, especially conisdering Mad's more cartoony art style, which I think Ultimates will suffer because of.
I can't comment too much on UXM as I've only really started to read this title again. I stuck with it for quite some time when it started out, and those original stories were outstanding, but I lost interest after a while. Kirkman is really impressing me with the Cable arc. It does have it's faults, yes, but nothing that really stands out as being a total bane to the series itself.
Overall, I agree with a lot of the ideas about time travel and especially, CLONES! That, and the dead returning to life. No need for it, especially now when the UU is relatively young. Maybe five or ten years down the line, you can have Beast and others show back up, but really, the credo of the UU in terms of that should be "the dead stay dead" for as long as possible. I think that the Marvel editors should also keep a short leash on the creative teams to make sure that any new (or new versions of) characters are handled well and not just a rehash of the 616 versions (which is a big part of Bendis' problem).