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This would be valid if there wasn't already a way to do this if you are jailbroken. This fact invalidates a lot of your post.
Clearly there are tradeoffs involved -- the developers of an app for a jailbroken iPad don't have the same concerns as Apple would. It's relatively easy to make a "hack" that forces iPhone apps to run in Retina mode on an iPad without taking into account things like memory usage, CPU usage and image quality. If the jailbroken app doesn't work, the expectation was pretty low anyway -- so the user just uninstalls the app and goes on. If it happens to work well for the apps they use, great. But if Apple makes a decision and it impacts the way the device works in a negative way, everybody is going to suffer for it.
I think the way Arn suggested (i.e, having a setting that said force 2x mode only for iPhone apps) would be a better solution, but it's un-Apple like in some ways since Apple wants to simplify the user experience. If anything, Apple could've just forced the 2x mode always - even pixel doubled, I find it a better use of the iPad display. But they didn't, and I suspect that memory usage had a big role in that decision -- especially on the 1st gen iPad.