First, I'm no longer having problems with the icons in the main menu not showing up. Also, the weird KeePass causes my screen to flicker issue magically got fixed when I did a clean install. Last, the Dropbox icon is showing up in my indicator applet. Over the past month, a lot of bugs have been fixed.
The focus-follows-mouse thing is still an issue, but I know focus-follows-mouse is not all that common. I have not opened a bug report about this yet because I'm not sure how important it really is to me. At work, I do not have focus-follows-mouse, and I use that computer (sadly) more than my Linux boxes.
There are still a few annoyances. In the launcher bar, custom menu items (menu items I've created myself) do not display the icons I've chosen for them, but the launcher bar is almost always hidden, so it's not a big deal.
I have a minor issue with the global menu. When my mouse is not at the top of the screen, the panel displays the name of the application that has focus. When I mouse over panel, the name is replaced with the global menu bar (the typical File, Edit, View, etc. menus). I think this behavior will be surprising to new users looking for their menus. New users will quickly get use to this; however, I just feel like this behavior is not very intuitive. It's a pretty minor complaint, but bugs me nonetheless.
Overall, Ubuntu 11.04 is going to be a pretty solid release. The issues above are so trivial that I almost feel silly complaining about them. The menuing system is much better than the old gnome way (old way being pre-Gnome 3). Screen real-estate is better utilized. The social integration works better than my previous install (more than likely, my old install was misconfigured). When Natty Narwhal is finally released, you should all download it, use it, and love it.