Including a controller means you'll probably see ports of a bunch of console/PC games, as long as the hardware is powerful enough to run them, and the devs tech setup makes an android port relatively easy.
Apple TV not including a controller, and forbidding devs from putting out games that require a controller, means that it won't get as many of these kind of easy ports. It also means it will be an attractive device for general consumers who don't have a particular interest in games, and will likely get lots of games that work fine with the included remote.