What I will say may be seen as impopular but I dislike thumbstick.
For fighting games, for 2d platformers, for FPS, thumbsticks are not optimal. It doesn't help most controllers now have terrible D-Pads.
So if I want to play Megaman, TF2 or Street Fighter I have no really good way to do it with the "default" controller. Sure it'd doable but I always feel underwhelming.
Of course, the Valve Controller may be a N-Gage kind of disaster but I'm trying to be optimistic here.
And like they said, you won't be forced to use it, or even use Steam Machines for the matter.
At least for now... but like I said, I'm being optimistic here.