I said it would break perfect compatibility, which it does. Apps that haven't been updated would run with black borders.
		
		
	 
They may not run with black borders, but perhaps with a linen texture or something else like a bigger status bar. There are multiple ways to use the extra pixels for something else. Even virtual buttons as mentioned are not completely out.
It's still perfect compatibility in the sense that nothing needs to be changed.
	
	
		
		
			It would only require higher resolution assets, and I believe everyone is grossly exaggerating the effects of upscaling images by a non-integer factor on a higher PPI display. I'd much rather have slightly blurry graphics in apps that haven't been updated yet rather than black borders though.
		
		
	 
They're not exaggerating it. GPUs and CPUs deal better with scaling factors that are power of base 2, so it has to be 2, 4, 8, 16, 32, 64, 128, 256, etc... Anything in between would degrade performance pretty drastically due to the need of using floating point math. That's why you don't see an AAx3 or AAx5 or AAx7... because those would introduce some insane performance hit.
	
	
		
		
			It would require more effort from developers, but 1440x960 wouldn't. They just change the scaling factor to 3, and then have developers re-submit their apps with @3x graphics and that's that. They've done it before, it was seamless.
		
		
	 
Apps with @2x assets would have to scale those assets to an arbitrary 1.5x scaling factor, and as I said above, that scaling factor would degrade performance.
	
	
		
		
			What if they want to change the resolution again in a few years? Are they going to go through that process again? Not to mention the 1136x640 resolution would prevent apps from running pixel double on the iPad.
It's a lot simpler to provide higher resolution assets than it is to alter the layout of your app.
		
		
	 
I don't think apps running pixel doubled on the iPad is an issue now that the iPad is already... in existence. The only reason why they needed the iPhone compatibility layer on the iPad was so that it wouldn't look so barren when it was introduced, but now that the iPad is already a product on the market, they can completely separate iPhone and iPad apps just fine.
I'm sure many developers are willing to write for both iPhone and iPad now anyway.
While it's a lot simpler to provide higher resolution assets, it's not simple to scale current assets, and that's the issue Apple would have to face if they were to choose an arbitrary scaling factor but decides to keep compatibility.
Edit: just as a side note, I'm sure you have noticed that John Gruber of Daring Fireball also agrees that 1136 x 640, or just stretching the length of the display, is the only way to do it. If you really need to know more why it is, I'm sure you can find more information from his website.