I'm an interface designer so I've really taken my time with Aqua and thought about ways to improve it. So here's a few concepts I've designed over the past year during my time with OS X.
I want a Dock that's customizable similarly to Cocoa toolbars. You could context-click the Dock and say "Customize Dock...", followed by a series of drag-and-drops to add smart items into the Dock, such as "Running Applications", "Quick Launch", "Quick Clicks" and of course flexible spaces (I want my trash in the lower right corner and everything else far above it along the right edge, anchored to the top right corner -- too much to ask?).
I'd also like to see persistent Dock menus. So even if Mail wasn't running, you could pop up its menu from the Dock and pick "New Message". It would then launch and pop up a compose window. Or you could Select "Play" from iTunes' menu and iTunes would launch and start playing the last playlist you accessed. This isn't even very hard to implement. The Dock app could just poke around a property list in an application's bundle to see if any menu items are available when the user control-clicks or right-clicks the app's Dock tile.
Another thing I want to see is Services in the context menu for easier access and better discoverability. Someone said this was in place in Jaguar, but it wasn't there when I tested it in 6C106.
I've sent these feature requests to Apple through their Mac OS X feedback form. If you like the ideas, I suggest you back them up by co-requesting them through their feedback form.