I _believe_ the Paramount aspect is just in distribution. That is, Marvel produces the movie however it wants it, and Paramount helps get it into theatres in exchange for a slice of the pie at the end. But rights deals are always ludicrously complicated anyway so I might have misunderstood it. Hell, Disney might want to keep its hands off just so they don't have to pay their lawyers for the time to figure out if they CAN put their hands on without getting sued. ;)

And even when under the same umbrella that doesn't mean things go entirely smooth for cross-pollination... remember all those stories about WB not letting Smallville or the Justice league cartoons use certain DC characters because they were being licensed by another group... within DC.