1. As people have mentioned, touchscreens were never designed around gaming. A standard gamepad with buttons and sticks works much better.
2. A big part of living room gaming is local multiplayer, about having your friends and family around you while you play a couple of rounds of Halo or Wii Sports. To support this, controllers must be affordable — common controllers are between $20 and $60 nowadays. You can't support local multiplayer when your controllers cost several hundred dollars.
3. AppleTV should be able to sell to people who don't have an iDevice. Requiring this would mean buying an AppleTV as a serious gaming platform would require, at least, another $199 for an iPod Touch. There are consoles that sell for less than that with a bundled game.
Third party gamepads exist for playing iPhone games on the iPhone (via jailbreak or iCade emulation), but they're not very elegant.
Controlling something on a flat screen while looking at a different screen puts limits on the number of "buttons" you can have and be able to push reliably. Also, holding an iPhone like a games controller would be uncomfortable over longish periods of time.