First off let me say I love my bike and there is nothing about it that I really dislike, but there are some area's that could be improved:
oil cooler, oil temp gauge, usb port on radio, iPod control through handlebar controls, angled valve stems, better seats, seat height option (I know BMW offers this option).
What would be a nice touch is if you could order your bike through the dealer like you can order a car. That wa you could have a bigger list of options to choose from and the bike could arrive how you want it, although I guess this would cut into to the dealers profits.