Super deformed chibi Trek.
Just kidding. I've been watching a lot of shoujo anime lately.

I haven't though about it before, but off the top of my head, I'd stick with the basic premise of revisiting TOS. However, I wouldn't put Nimoy in the film. Have him on set as an adviser, sure. Shatner too. But keep them out of the film proper.
Since framing a Trek film around a villain has generally been a failure (Khan excepted), maybe I wouldn't have one, instead doing something like TMP or STIV, where the heroes have to deal with a situation rather than directly overcome a scenery-chewing bad guy.
Ideas others have posted that I like: getting a good SF writer to work on the story, adapting a Star Trek novel (although I would go with a TOS novel instead of a TNG one).
I would definitely have: space exploration, going where no man has gone before, presumably as a lead-in to the plot.
I would definitely not have: time travel, threat to Earth.
Things I definitely would never do: revive TNG, anything in the 24th century, or go post-Nemesis.
Something else that I might do is re-imagine ENT. Through out the crappy series, start over from scratch, and do it so it doesn't suck.
Idea #3: Adapt
Strangers From The Sky as a two-part miniseries.
Marian