Thor really was just a delusional Norweigan nurse with stolen technology......Until Scarlet Witch altered reality to make Loki, Asgard and Valhalla real. That's why his speech changed from contemporary to pseudo-Elizabethan, and why he suddenly acquired an arsenal of alternate hammers. Wanda probably was responsible for Valkyrie getting powers, too.
The creepy Spider-Man-Who-Is-Not-Spider-Man from Ultimate Avengers...
The mysterious female shadow behind Quicksilver in Ultimatum: Requiem is...
The Ultimate Super-Soldier Serum was derived from studying the Chitauri.Herr Kleiser had super-strength and a Healing Factor roughly similar to Ultimate Captain America's. What with the UM's tendency to give everything a Meta Origin, it makes sense to tie the last few remaining loose threads together.
Dr Manhatten created the Ultimate Marvel Universe.The world of Watchmen is dark,gritty and realistic,and the Ultimate Marvel Universe is darker than the normal one.At some point,Dr Manhatten decided to create his own world(similar to the WMG about Superman),however its tone reflected his own gritty and realistic world
Ultimate Wasp knew some Brother-Sister Incest couplesmaybe some were some very good friends of hers.
Nick Fury was not killed in Ultimate Avengers vs. New Ultimates ...It was and LMD.
Ultimate Magneto actually had a secret Freudian Excuse.616!Magneto is sometimes speculated to have some variety of psychic power in addition to the magnetism. Ultimate Magneto had some kind of low-level telepathy or empathy that he never consciously recognized and developed, which left him open to the psychic impressions around him. Considering that the Ultimate Marvel universe is full of jerks, being a psychic sponge at an impressionable age didn't do him one bit of good, and aggravated his preexisting mental instability and supervillainous tendencies. Having to deal with the cast of The Ultimates in my head would have me tempted to start flipping the magnetic poles.
Ultimate Carol Danvers will become President of the United States.With no current signs that she's going to become Ms. Marvel like 616!Carol, but instead having led SHIELD and now being the Presidents Chief of Staff, it seems like the door is open for her to lead the country considering she might be doing so de facto anyway if the current President isn't interested in running for election.