When you reach the end of the mouse pad, you need to lift the mouse and return it to the center of the mouse pad. It's annoying at first, but I got used to it after a day or two. Now I don't even notice. If you already lift your mouse higher than you need to, you won't notice any difference. Another issue with optical mice is incompatibility with certain surfaces.
Reflective surfaces confuse the camera on the optical mouse.
Hardly a problem in putput-ing around in Windows, but a BIG problem in games if you don't know how to set up the game correctly. A typical mouse, if moving ultra-quickly, may be overwhelmed by the movement and not be able to map all points between the start and end of the twitch, but the destination stays the same since the mouse never loses track of the ball. What this translates to on screen is some semi-jerky movement, but you end up where you wanted to go. An optical mouse, on the other hand, has no ball to reference to. The optical mouse takes thousands of pictures every second, but if you suddenly whip the mouse across the mouse pad, the mouse has problems differentiating between a bunch of blurred pictures, so it gets confused.