Yamaha FZ6R
Is the FZ6R boring or just silky smooth? In this company it falls between the clamorous Ninja and the aggressive Suzuki, and with those two extremes already assumed we can easily designate it as neutral. That means there's a lot of room for improvement but no major objections.
At its heart is a perky motor with lineage from the R6 line, and that means there's some potential that the factory has concealed. Styling could use some work too, but with a little effort the FZ6R will be right on track to ride with the cool kids.

Swap stock for an adjustable...

Swap stock for an adjustable lever,

then lose the hideous exh...

then lose the hideous exhaust

and upgrade the brakes for...

and upgrade the brakes for a much-improved FZ6R.
SUGGESTED MODS
Rear sprocket (-1): Vortex, $74.95
Yep, you read that right! We'd actually remove a tooth from the rear sprocket. First gear is too short, and at highway cruising speed (70-75 mph) the revs are a bit high. Considering both those issues, a simple solution is to change the gearing. With a color coordinated CAT5 sprocket you'll have a smoother ride with sweeter looks.
Full exhaust: Two Brothers, $999
The stock exhaust weighs over 18 pounds, while a Two Brothers full system is just over eight pounds. You can do the math on that one. Peak power should increase by about five HP, and you'll get a fatter midrange along with sound enhancement and an obvious style upgrade.
Brake lines/pads: Galfer, $98 (lines), $40 (pads)
The stock brakes simply leave a lot to be desired. But, with steel lines (color coordinated, of course) and more aggressive pads the performance will be increased significantly.
Levers: Pazzo Racing, $199
A non-adjustable clutch lever not only looks cheap but doesn't allow for quick and easy adjustments. Sorting the lever situation is as simple as installing a set of adjustable units that are custom tailored to your preference.
Fuel management: Two Brothers Juice Box, $299
You'll get performance improvements out of your aftermarket exhaust system, but to get it working at its best you'll need some fuel management. The Juice Box is easy to install as well as tune.