The terms 2D and 3D, when applied to how they used depth of field in the two versions of Up, is a bit disingenuous. It's more accurate to describe them as Flat and Deep. If you're expecting 3D that leaps out at you, like Coraline or My Bloody Valentine 3D, this isn't anything like that (thankfully).
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I've seen Up both ways now (original pre-Cannes writeup here). I plan on seeing it again at some point theatrically, and I won't be disappointed if I can only see it Flat. I liked that I could see greater detail at greater depths in parts of the picture, but it did not substantially transform the experience for me. Honestly, I think I prefer it Flat, if only for not having the too-small glasses caving my head in from the sides. After my Deep viewing of it, I commented to my wife that I ought to engineer my own custom 3D frames.
Up is great to watch either way, and I think they may have made a misstep not looking at more comprehensively merchandising it. Little figurines would go over huge. They may not think so yet, but plenty of people would gladly put Carl and Russell on their desks at work.
Particularly because it plays so well for older audiences, it could have stronger legs than Disney has projected. Other 3D stuff will fail through the rest of the summer, Jonas Brothers-style, and Up will get those screens back. Dinosaurs or no, Ice Age 3 isn't going to get over the hurdle of Fox forcing theaters to pay for their own 3D specs.