I think people give Eisner a much harder time then he deserves, the guy made Disney more profitable the people could have imagined. The thing was that he was a TV guy not a movie guy so he more or less shifted the focus of Disney from movies to TV and the Theme park.
And to be honest it's not hard to get Steve Jobs to throw a fit, he may be creative but he's never been known as someone who's easy to get along with. Eisner was the same way so you basically have two people that are very similar in that regards so conflict was bound to happen.
I see the Pixar acquisition oppositely then the other people here, I see Disney just picking up the flavor of the month instead of trying to fix their problems internally. Maybe having Jobs on their board will help fix some of those problems, though I doubt it since their problem is not something I think Jobs could fix or would want to. What I see as wrong is that Disney is a traditional institution, what I mean by that is you can expect (or should) expect certain things from them like their "traditional" animation and family movies, I see Disney moving away from that traditional mindset which people expect.
There's room for both the flashy, "hip" pixar or Dreamworks stuff, and the traditional Disney stuff. Now yes some of Disney's problems does come with the scripts but the problem I've seen with their animation is that they don't know what they're supposed to be anymore so the movies come across confused and not as focused as they should have been. And this hurts the sales due to it not finding the audience because no one knows who that audience is or they're something so different that while they find an audience, Emperor's new grove for example, the movie turns off the parents because they expect something else.