To me, fan input should be taken in very few ways. The main one would be game success - if a game is popular, explore options like a sequel or a similar game. If people like a soundtrack of a game, give the composer more work. If people like a battle engine in an RPG, keep it handy for another RPG (or a sequel). But you can't sit people down in focus groups and ask them what they want - as mentioned before, look what happened to the X-Box controller. If there was some magic tool that could sum up the opinions of everybody and make an average out of it to find the best way to please the most people in the greatest way, then you could listen to the people. But until it's invented, there is a reason these people have their jobs. Because they know what works.
I think the episode of the Simpsons where Homer helps Mel Gibson make the movie is a perfect example. Look at the changes Homer made. He thought they were great, and so did Mel (and so did I), but the people hated it. You can't take random opinions and use them to please everyone, so you gotta let the professionals work and hopefully please most of the people.