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I do think there are improvements being made.
Also, more and more PC gamers also have a controllers now too.
Finally, and I know this is obvious, but there are fundamental input differences between controller versus mouse and keyboard.
In many cases, you are at least doing 1.5 to 3.0 times as much work to support both input schemes at the same time. Some games, like FPS's have it easier, while some, like ARPGs, are much harder.
Witcher 2 is really a poster child of this sort of UI compromise.
I'm not quite as optimistic about this front. The root issue is that mechanics are designed for certain UI devices. You can certainly make mappings for other devices after the fact, but they will always feel that way.
Even FPS games are fundamentally different games when played with K&S v. controller when one takes into account the auto-aiming and other assistance mechanics baked into the game.