One good reason I have for using mic-in over line-in is that, on my Edirol at least, the line-in plug seems especially touchy. I have yet to make a recording with line-in that wasn't affected at some point by "static" - i.e., the noise you get when plugging a live guitar cable into a powered amp.
Granted, I'm not the nicest of tapers - I tend to keep the unit in a breast pocket, and I do occasionally move about. However, even the one time I had the unit "at rest", I was left with an incredible amount of noise (note - I don't mean "line-noise", or "hiss"). It was an unamplified classical quartet, hardly the loudest band I've recorded.
Even once when going from a matrix feed, I still ended up with static.
Mic-in, on the other hand, works fine.. though most louder shows end up a little muddy, even with the low-cut on.
And, btw, it's pretty easy to overload the on-board mics... just record any act that even approaches metal.
I have a recording I made with the input level at 1 that's still on the brink of distortion. Can't remember if I used the low-cut, tho...
I'll upload a few samples later tonight, or tomorrow afternoon - right now I'm on my way to a show.