I'm... just...confused. Really. I think Marvel was in strong enough shape to stand by itself at this point. I agree about those movies, Sony pressured them to put in too many villains (Venom especially) in Spidey 3. But these were partnerships. This is a buy out. It sounds like it could go either way.
On the plus side, Disney has no excuses and no problems releasing the Saban produced Marvel cartoons from the 90's that Disney owned ever since they bought Fox Family (Curse you, Rupert Murdock). They've been releasing the X-Men series so far.... I guess that was a sign. For the longest time, Disney and Marvel had bad blood over these shows. Disney made a HUGE error in not releasing any Spider-Man DVDs when the third movie rolled around. Thankfully, they didn't have the same mistake when Wolverine came out, releasing the X-Men ones.
But what I'm worried about is future projects. Spectacular Spider-Man is pretty much on thin ice. I doubt we'd see a season 3 (Kid's WB has a large amount of blame in that). heck, Bulgaria got season 2 before us. BULGARIA! And I just hope Wolverine and the X-Men are on solid ground too (I've heard very good things about that one).
All and all, I hope they run them like a separate company. Warners doesn't really do that with DC... and we lost the 1960's Batman TV series as a result of rights. And I'm also concerned about Boom comics' Muppet and Pixar comic book lines. Will they continue, or will they be absorbed into Marvel?