These features bug me about Lion:
Inverted scroll - This makes sense for an iDevice because you're interacting directly with the page or object you're manipulating, but for a trackpad it's different. Besides, I've been scrolling down for the past 20 years, but now I've got to change.
Resume - This feature is dangerous for Quicktime... I was watching some "vacation videos of my wife and kids" and I had 4 clips opened at once. I press cmd+Q to quit. Later when I opened Quicktime, all four clips popped right up on screen again! To clear the history, you have to close each window individually before quitting the app. But that's still not the end of it. When ever I do App Expose for Quicktime, the bottom of the screen shows a history of all the clips I've opened and I can't erase it. I tried going to Quicktime>File>Open Recent>Clear Menu, but that still didn't work.
Mission Control - Expose was perfect because it was good for both navigating your apps around the desktop and also for displaying full view of all your apps. Mission Control can only do the first thing.
Quick Look - The new grey window looks more like an app, rather than the previous HUD with black transparent background. However I do like that when you Quick Look an HTML file, loads the webpage.
Gestures - three finger swipes use to be back/forward for every app, now it moves between spaces and full-screen apps, Pinch to bring up Launchpad is difficult on my tiny 11" MBA trackpad, ladies with long finger nails can just forget it. Personally I think this gesture would make more sense to make apps full screen.
Safari - no gesture or shortcut for private browsing and tab navigation, no Google search image preview (there a plug-in but it's buggy), still not many plug-in and no themes
Dashboard - not many good widgets, many old ones are not compatible with Lion
Launchpad - 1) There's a limit to how many apps you can group together. 2) The 2-finger swipe to go to next page which is confusing compared to the 3-finger swipe for moving around Spaces and full-screen app. 3) Like how iTunes has an option to organize your music folder, Launchpad should also organize your Applications folder.