The Marvel-Disney buyout's major problem isn't necessarily creative, but one of flexibility and the further ghettoization of comics. As a comic company not previously owned by a large media conglomerate, Marvel was allowed a considerable degree of creative autonomy. Unlike DC, who have always been more conservative in promoting new ideas due to their ownership by AOL Time Warner.
Even though Disney and Marvel have both stated that there will be no editorial interference -- the Punisher will still use the ol' ultraviolence on thugs and criminals everywhere -- Marvel will still have to answer to their mousey overlords.
This means that Marvel won't be able to take as many risks with comic book series, or even allow relatively unpopular series to find their audience. Expect less issues like Strange Tales, an anthology book featuring some of indie comic's best taking on Marvel's characters in outrageously off-beat ways. Series like this just won't fly in the new Disney order.
Another problem is the fear of overtaxing the Marvel brand. Disney was known for driving their properties into the ground under old CEO Michael Eisner -- see Bambi 2 and The Fox and the Hound 2, which were already in production during his 2005 ousting.
While current CEO Robert Iger has been less likely to rapaciously utilize beloved past properties, it's still a potential problem, especially considering their newly acquired licensing bonanza. Anyone who reads Marvel's comics knows about the sheer amount of licensing already going on. Toothbrushes, bedspreads, backpacks, trucker hats with comic panels on them -- these are all items you can buy, each festooned with Marvel characters.
Now that Disney has their fingers in the pie, expect to see even more influence in the production of Marvel merchandise. This may, in fact, saturate the market with a huge blanketing of Marvel paraphernalia. While this isn't aggravating from a business perspective, it does lessen the overall value of the characters.
No one thinks Disney characters are even close to approaching high culture, mostly because marketing has specifically made them part of "low culture." Comic book characters, already viewed as low culture, become more ghettoized as their current low relative merit is further decreased as they become nothing more than merchandised money farms.
Marvel Comics has tried, to varying degrees of success, to be thought of as a serious literary institution. It's even less likely now, because people will associate Marvel even more as a non-experimental, boring and staid super hero comic book outfit -- like their competitor DC Comics.