I agree that the set up of Future's End tends to drag down the rest of the episode. Like Godben, I find it incredibly unilikely that Voyager could do something like this to a 29th century ship. Either 29th century tech ain't all that, or the pilot was no good.
I think Futures End is kind of fun though. I enjoy seeing the Voyager characters in (what was) a present day setting. There is no denying that Star Trek IV did the whole thing much better though, with much more humor. Ed Begley Jr. does a nice job as Starling.
You kind of have to turn off your brain to enjoy most Trek time travel episodes. They are so all over the place with their rules. I (for the most part) am able to enjoy the episode for what it is.
This is complete bias on my part, but Sarah Silverman really brings the episode down a bit for me. I just can't stand this woman, she is like nails on a chalkboard to me anytime I see her.