It comes down to this... This will either be great for Disney, or horrible for Pixar. The potential for great is that we could get a creative, vibrant Pixar, with even more resources at its disposal, and a Disney who re-learns what creation is all about. The potential for horrible is that the Disney machine is just too unwieldy to accept that kind of change, and when the Pixar unit has a slip-up (as everyone does eventually), its culture and creative method are squashed.
Which will it be? Only time will tell. Yes, some of the key Pixar people are in apparent positions of power, but are they really committed to not only maintaining what Pixar does, but also spreading that to other creative areas of Disney? Is Iger truly committed, or did he just make the only move that could save his job? If they are committed, can they pull it off? Will they stay true to it when something fails and the Street calls for "safe"?
Like I said, time will tell.
On some of the details...
Pixar succeeds because he lets Lasseter create and doesn't try to be Walt Disney. When Eisner fancied himself Walt and Roy all rolled into one he started getting into trouble. I think Jobs would have the same potential.
While I agree Jobs = Eisner 2 is a possibility (probably moreso than Iger ever being Eisner 2), he has at least shown the willingness to let people like Lasseter do their job, as you noted. Something Eisner became increasingly unwilling/unable to do. I think that there is a pretty good chance Jobs will continue that way of thinking.
Though, that brings up the fact that at least at this point, he has nowhere near the power Eisner had. Yes, as noted, he is the biggest shareholder, but at 7.something percent, he will have to be heard, but certainly not obeyed.
Yes, he will also have a board seat, but Roy/Stan held two, and look where that got them.
He apparently won't have any direct management responsibilities, which is obviously unlike Eisner.
On the other hand, he won't have to deal with an all-powerful Eisner either, as there is no such entity.
So IF Jobs really wants to initiate significant changes and/or initiate some kind of power play in the future, the key, I believe, will be his ability to win over other large shareholders (like Roy and the mutual/pension funds, if not Eisner), and influence other members of the Board. Who knows, perhaps he has already done this, or at least planted some seeds.
Then again, perhaps he has no intention of stirring things up, and really is going to focus on Apple and be just another director.