I'm not sure how tying up your iPad or iPhone via AirPlay video or mirroring is a win for users. It's very geeky compared to just selecting an App off the Roku, Hulu Plus off XBOX Live, etc...
It isn't as "geeky" or tiresome as trying to control a cursor position on the TV with a regular button or traditional keyboard.
You're going to need a more advanced input controller if you really want to put a variety of different apps on the Apple TV. We aren't talking just about video playback here, the current Apple TV does that just fine and will continue to improve with changes to the iTunes Store and offerings direct from Apple.
However, with other types of functions the existing three-button IR remote just won't cut it. In that case, Apple wants you to use a hand-held iOS device and if you mirror the display you get both the control
and the ability to run just about any app that currently exists for the iPhone/iPod touch/iPad. That's the way Apple is going to do it, they aren't going to require a completely new class of apps just for the Apple TV.
Look at the Google TV and the Boxee Box. Both require some type of dedicated keyboard or controller for their more advanced functions. If the Apple TV is going to be anything more than a video playback device then it needs a similar controller and the touch-controlled iOS devices are miles and miles ahead of anything that ships with either the Google TV or Boxee Box.
You should think of the Apple TV as a kind of loss-leader, just a basic and inexpensive display adapter to go between your TV, iTunes, iCloud and/or the iPhone/iPod touch/iPad. Those other products are what Apple really wants to sell, not a $99 Apple TV that may eventually have to compete at an even lower price point.
Thus, I continue to believe that there won't be any kind of app store for the Apple TV. We will have apps for the other iOS devices that will mirror to the Apple TV.