There are a few reasons why the new iPad would do this and the old one doesn't. The most basic reason is that on Retina displays, apps run with Retina assets if available. Non-Retina displays never use Retina assets. In this regard, the new iPad is behaving exactly the same way as the old ones.
Second, if Apple did decide to use the Retina graphics for 2x mode on older iPads, it would introduce a few problems. One is that the original iPad is memory starved as it is. It came with 256MB and it wasn't until the iPhone 4 with it's Retina display did Apple bump up the RAM to 512MB. Second, should Apple use the Retina graphics for both the 1x and 2x modes? If they do, they are wasting CPU and battery to produce pixels that will only be scaled down. If they don't, they would need to come up with a way for apps to switch between 1x and 2x mode at runtime (they currently can't -- there is nothing in the API to even allow for that possibility). Also there is the issue of how the graphics would look when you take Retina graphics and scale them back down to 1x -- it's not nearly as nice as simply using the 1x graphics already.
One more thing to consider -- when the original iPad came out, there were no Retina display devices. All iPhone apps were 1x apps. The pixel doubling mode of the original iPad was just a way to allow iPhone apps to take up more of the screen than they would otherwise. Clearly Apple's goal was to have more iPad native/Universal apps. Spending engineering resources to make "legacy" apps run better is typically not a good use of time. Turning on Retina support on the new iPad for iPhone apps didn't require a large amount of engineering time. In fact, due to how the iOS APIs work, it may have not even required any time to get it up and running. Just the time required to verify that it did work okay.
This makes sense. I didn't even know that the iPad 2 ran retina iPhone apps at 480x320! (I only had the iPad 2 for 14 days, then returned it because the Verizon network was too slow. The AT&T model was still out of stock, so I never got another iPad till this 3rd Generation iPad.) Anyway, I never noticed that the older iPads ran the non retina iPhone app resolutions. That would be awful if this were still the case,
16 pixels on the third generation iPad would be used to show
one pixel of an iPhone app!
When I saw iPhone apps running on my "new" iPad, I just assumed that all iPads ran the iPhone apps at 960x480. I could see on the new iPad that
4 pixels were in use for every
1 pixel of an retina iPhone app, but what's really cool is that inside the iPhone Apps showing PDFs, it's full native resolution, meaning 1920x960 pixels are used for showing PDF content, and perhaps any regular text (non bitmapped graphics/text).
Had I known that the older iPads ran iPhone apps at 480x320 resolution when doubled in size (crazy!), I would have created this thread on Friday, March 16, when I got my new iPad in the mail! I simply assumed Apple had put retina resolution iPhone apps on the iPads from the beginning (when iOS 4 came out). I don't think RAM would have been the issue though.
It does seem possible that Apple was encouraging developers write an iPad version of their iPhone apps. If an app can make more use of a larger screen, then that app would inherently be better on the iPad. Double sizing iPhone apps just makes objects (buttons, etc.) bigger than they need to be, instead of adding more objects if applicable. The iPad screen
area is 7.7 times greater. I've seen how Apple compares the iPad apps to Android apps designed for the phone running on tablets, and how an app designed for the larger iPad screen is much better than a double sized Android apps on the tablet counterparts. I think one great example is Facebook. The iPad version of the Facebook app makes great use of the extra space (and it took quite awhile for it to be released).
Perhaps if Apple had let the retina iPhone apps show 960x640 natively on the iPad 1 and 2, there would have been less pressure for the developers to create iPad specific apps since only 28% of the iPad screen is window boxed when apps are native at 960x640.