I think it does come down to color, since I'm on the hunt for a white/mocha combo and I can't find any for the price I'm looking for. If I one day decide I want either firmware, I know how to get them.
I haven't used ME or IE, but from what I've heard, I'd rather have vanilla. I don't like the idea of the music player always being open or my media key being specific to the Web application.