What is your intention for the bike, it really depends on what you will be using it for. Are you interested in rideability improvements, looks, both? Will you be cruising around town, riding canyons, going to track days? Comfort, power, handling, cosmetics, etc., lots of areas can be improved, all it takes is money. There is no wrong answer, we are all riding for different reasons and motivations, but knowing what you will be doing with the bike, people can make their recommendations based on what you want out of it.
I can't stress this enough, the first thing you should do, and it's completely free, set up your controls to fit you, adjust the clutch and brake levers, adjust the shifter and brake levers on the rearsets. The last thing adjust the suspension for your weight. Just doing these little things will make the bike more enjoyable.
But as Vansmack said, it all comes down to what your plans are with the bike.