1. Startup time. I just ran it twice on my machine. First time it took 20seconds before showing the splash, then 10 seconds after that (I'd never launched it before). Second time it took over 5 seconds to launch completely
2. Cluttered UI. menu bar + status bar + project explorer + tasks + outline take up between 20 and 70% of the window depending on how big I have the window (god help me if i try to use it on my old laptop with its 1300x700 resolution)
3. Difficulty of editing stand alone files. It's just a pain in the arse editing files that aren't in the project, and that you don't want to be in the project
For comparison, sublime text 2 launches in <1second on the same machine, and that includes restoring 100% of the previous working state, including unsaved changes to all files, even if the computer crashed and it wasn't closed down properly.
edit: I almost forgot
4. It also takes 1-5seconds to close.