Are you familiar with the term 'bonus?'
The current AppleTV comes with a remote. It does everything I need it to. But sometimes I whip out my iPhone to control it because it's faster. My wife does the same. Or perhaps we use my daughter's iPod. They'll all do it, but the original remote is still sitting there if we need it.
How is any of that a bad thing? I've never thought "this isn't working well!"
Because this kind of self-centric answer assumes that everyone has the same situation- lot of iDevices in each household so that you can take yours with you and others can use theirs if yours is out with you, etc. That's not a typical household, yet this is a product that could appeal to households that lack any iDevice.
While I expect it to come with some kind of regular (non-touch) remote to cover that base, all these dreams of existing apps running on it probably won't be compatible with anything short of an iDevice remote.
There's where the problem in imagining the combination starts showing itself. Another is that all apps dependent on touch require you to look where you are touching (on the iDevice screen). So, while one can imagine the visuals appearing on both the little screen in your hand (so you can touch the right spots) and the big screen in the living room, any apps- especially games- that involve a lot of touches to play well will pretty much force the user to keep his/her eyes on the little screen in his/her hands vs. the watching the big screen. If you are alone, why bother with the big screen? And, of course, I don't imagine Apple delivering a new iTV AND a touch screen remote control for $99; the latter would have to be "*sold separately" if the iTV comes out at only $99.
Thus, my guess would be a classic remote for the principal controller- one with raised buttons so that you can keep your eyes on the big screen while feeling your way to whatever remote control option you want to launch. However, that is unlikely to solve the latter issue with touch screen apps- especially apps that require a lot of touches (like games).
I do agree that since we already have remote apps for iDevices, there is likely to be a "bonus" with this such that the remote apps will control a new iTV much like they control the old one. I just don't see it- as implied by this article- that an iPad or similar will be THE remote for the new iTV.
Or is this going to be like airline tickets (soon). You can buy your ticket to fly anywhere for only $1*
*Other fees apply (but you won't find out about them until you are checking in at the airport ready to board the plane).