I hate the 3D dock for 1 reason: If a window is behind the row of apps that stick out over the dock itself, it can be a pain to click that area of the window. This is because the actual boundary of the dock is an invisible layer on top of the actual app icons. If you click anywhere within this layer, you open an app. If you're in the middle of a busy workflow, you find yourself making this mistake more than often.
I know you can hide the dock, or make it smaller, or even move it to the side, but I prefer my dock in view, at the bottom. I hated the dock ever since Leopard. Glad they put the Tiger dock back.
In fact, I haven't been this excited about a OSX release since 10.5. I'm happy Apple still cares about the Mac and is taking big steps with it.