There need to be more marvel books that make it easier for new readers to jump in. Character personalities completely changing because of something that happened in another book makes for an awful narrative unless you read both, and if you follow that web through the marvel universe, it basically necessitates either being a hardcore fan or giving up on trying to understand comics altogether.

I hate anything in comics where the explanation is "magic" or "mystical" without it being spun as technology too advanced for us to understand.

Comic book writers should just stop trying to kill characters when they know someone, if not them, is just going to bring them back eventually. It ruins the impact when you go read the original story wherein they died.

On the ultimate side specifically, I think Ultimatum was a godsend, and did wonders for making that line truly unique. I hated the pattern of "616 villian, but then sort of different." The post-ultimatum world truly made two separate, unique universes with their own stories to tell. If killing off half the characters is what it took, then thats what it took.