C'mon, many people who plays PC versions of most console ports will tell you that there is a problem here... The other big offenders are often "Games for Windows" games.
IIRC, the latest GTA game wouldn't even let you use a HID compliant controller, so it was either an XBOX joypad (Or XBOX steering wheel) or nothing.
I kind of sympathise with the above comment ("What about the device maker?") but think that it shouldn't be the device maker, but a responsibility of the OS. MS made a great advance with the HID compliant system in the past, so it should extend the idea and let you remap HID controller mappings on a per-application basis.
Having said that, there would still need to be effort from the game manufacturers. For example, many games do not allow you to map an analogue input method to an analogue scale (eg allowing analogue handbrake in many racing games is not common) so that needs sorting out too.
I suppose apart from disabled people, there are probably not that many people who care too much, but for me I hate the interface to ruin a game. If I have to stop playing to look at the keyboard to find a key - that's game over to me. Hell, even moving my fingers from WSAD to hit 1,2,3,4 or something annoys the hell out of me. That's why I use XMouse (highrez.co.uk) to program mouse wheel u/d/l/r to 1,2,3,4 (you need a tilting wheel.) Great for battlefield - all 4 weapons / gadgets available through one roll or tilt of the mouse wheel ;)