There's always been lots of time travel in the Trek universe, how about one involving a ship trapped in the past? Maybe the far distant past, when the Q were still evolving? I'd love to see this--something where all the most powerful and advanced races were still in their infancy, just getting out among the stars.
Or, how about a Trek trapped in the future--the Federation has fallen, and the ship is weaker (to a significant, but not crippling, degree) than whatever race/federation/etc. is currently running things.