When you navigate via keyboard (by pressing "f"), Vimperator marks links with numbers, Vimium marks them with letters, from ("a to "zz'). Letters are much nicer when you can touch type and your hands are already on the keys.
Vimperator used to do silly things like hide the address bar and force you into doing everything in a kind of "command mode". It never felt very smoothly integrated with the browser and it was always a pain to try and open a new site via command mode instead of just using <Ctrl>-L and typing it in the address bar. Invariably I would try to type something in a textbox or use some keyboard shortcut, only to find that Vimperator hijacked it and I'm now typing in command mode.
Vimium doesn't give me these problems because it doesn't have a command prompt/mode. Besides that, it's integrated very nicely with chrome, in such a way that I can use normal keyboard shortcuts as far as possible, but have vim-like shortcuts for the things that matter (e.g. "/" for searching, navigation via keyboard etc.)