Pros
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The Return of Hand-Drawn Animation: Bringing back the basic building block of the Disney heritage was the most important mission of this new regime. Just the mere fact that this revival was engineered by
computer gurus, whose films were falsely inspiring 2D's "death" shows how boneheaded the decision-making of Eisner's latter tenure was by the time he left.
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Quality Control: The track record for Disney's features have been more consistent, both creatively and financially. There's still a way to go for Disney to catch up with Pixar and DreamWorks' records, but if Tangled is any indication, audiences are steadily regaining confidence in Disney storytelling.
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NO MORE CHEAPQUELS: This was the smartest decision Disney had made in a long time. These sequels, despite the later ones pushing for better art, still dilute the strength of the original stories, and they decrease the originals' long-term value by constantly being promoted alongside them. It had reached the point where the prospect of making endless sequels had become a bigger priority than making a decent original, not to mention that they contradicted Eisner's "2D is dead" claim in a major way.
An interesting story behind this is that because the planned Chicken Little sequel was cancelled, so too was a planned TV series to tie-in with the sequel. This caused Phineas and Ferb to finally emerge from development hell.
Cons
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Where's the Shorts?: Four years into the rebooted shorts program, and only one has been released theatrically. One had switched to the TV format, and became a surprise hit.
But what about Glago's Guest? And the Ballad of Nessie? And Tick Tock Tale? Why was one withdrawn from public distribution? Why are the other two taking an eternity to go into production?
Seems like whenever Disney tries to make shorts again, they drag their feet with them.
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Little Innovation: Some technical CGI experiments have been seen with Bolt and Tangled. There doesn't seem to be enough of it in storytelling. The most infamous case was Chris Sanders' falling out on American Dog.
This isn't the same as quality, as this now calls for doing something different to prevent monotony in their product.
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Brain Drain: Many talented artists are still leaving Disney, while DreamWorks is becoming a safe haven for those chased away by the Mouse. Again, Chris Sanders is the best example. Who knows how well American Dog could've performed? The fact remains that Sanders along with Dean Deblois, both from Lilo & Stitch are now making a ton of money for DreamWorks instead of Disney.
Disney has actually had this problem since the 1980's, with Lasseter himself being one of those who left. If Disney learns how to keep and nourish the talent they already have, they could spend significantly less money trying to buy them back later, like they did with Pixar.
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I should admit that at first, Pixar's merger with Disney gave me mixed feelings. It sent the message that Disney was somewhat incapable of making good movies on their own again. That they needed to swallow up a more successful competitor to stay in the game.
Pixar was saved the headache of trying to find another distribution partner, where there was no guarantee that they would get nearly the lofty relation they had with Disney. (I'm looking at Warner Bros.' terrible track record with animated features.) But it also created a slight concern, given Disney's corporate environment that Pixar would someday succumb to that deadly culture.
Looks like, overall, while life is not perfect for either studio, things are much more stable than before the merger.