The problem is that touchscreen and controller usage are so completely different that you basically have to design games intended only for use with a controller add-on.
...which leads to a chicken and egg situation. If Apple were to create their own standalone controller, I'd guarantee you'd start seeing games come out that take advantage of it. Thing is, until Apple sees a compelling reason for doing so, they won't make it, and people won't make games to support it, which means Apple probably won't see a compelling reason to make one.
And that is not a great business to be in wrt tablets, which are supposed to be complete in themselves (in most people's minds). So, not many have made games for such things, and many of those are retro stuff.
I'd think of it as an accessory similar to the bluetooth keyboard. You can use the iPads onscreen keyboard for typing, much in the same way you can use onscreen analog controls for games. It doesn't hurt the core experience at all. People who want to do heavy typing on their iPad can buy the keyboard, much the same way that more dedicated gamers can buy the controllers. The more casual people? They have the touch based controls ready for them at any given time right out of the box.
Or to put it more simply, as long as everyone isn't required to buy one, it won't hurt people's expectations of the iPad at all.