I'm transferring from NYCOM to KCOM in the fall (to start my third year). It really wasn't that big of a deal. I didn't get the third degree about my reasons, and faculty and deans at both schools were very helpful. I'm transferring because my girlfriend matched in St. Louis, and because of the economic insanity of trying to live off student loans in NY. My main advice is to start the process early. I initiated contact with KCOM in December, and it was June before all of my letters got sent out. In fact, I could have transferred this year except that by the time KCOM finally scheduled an interview, NYCOM was already in session and wouldn't refund my tuition.
to sum up, transferring is doable, but it can be very time consuming, so get the ball rolling early.
Good Luck