Actually they do not look exactly the same, for two reasons:
1. Some iPhone apps get scaled using a bilinear filter, not pixel doubling. I'm not 100% sure what determines which scaling gets used, but I suspect it's related to whether an app uses the standard UI elements and/or hides the status bar.
Examples: Game Dev Story, Bookworm, Dungeon Scroll, Critter Crunch, Angry Birds before the Retina update. In fact, if you look closely you can sometimes even see the switch between the two modes during the app splash screen.
2. The subpixel structure is different. When pixel doubling, you basically get pixels with 12 subpixels instead of 3. Their shape and spatial arrangement is different, not to mention the gaps between them. On the 3GS display our eyes are actually able to "see" the red, green, and blue subpixels, but they see each color as a dot. With four subpixels of each color distributed over a larger area, however, our eyes actually perceive the (upscaled) pixel as having an area. This is due to the way our eyes/brain filter the signal they receive from the millions of rods and cones on your retina.
On the one hand, this makes the iPhone 4 display look much more uniform and "paper-like" than the 3GS display, especially when showing large areas of flat color. On the other hand, it gives upscaled pixels a much more square-ish look where the 3GS pixels appear more like a rounded dot.
The microscopic structure of a pixel can make quite a difference on how we perceive an image on the screen. See this for a somewhat related example: http://www.tested.com/news/up-close-and-personal-with-the-kindle-and-ipad-displays/717/
either-way, 720p media will look the same on a 2048X1536 ipad, as it would on another tablet with a 1280x720 or osmeting