I have been thinking a lot about a d20 Star Trek setting for some time. While I was vehemently opposed to it initially, I've had several years (and two iterations of Star Trek RPGs) to adjust my way of thinking.
I don't think that I'd use the D&D rules for a Star Trek setting, or even the Star Wars rule set. Probably I'd use a version of d20 Modern with d20 Future, but I'd use the Damage Saving Throw mechanic used in Mutants & Masterminds, the greatest superhero game I've seen in years. This allows for high-level, highly-skilled characters that can still be wasted by a single phaser shot, particularly if the character is a non-combat type (or the player is a lousy roller!).
As for playing alien characters, D&D allows for this (after a fashion) using ECL and Level Adjustments.
Certainly the d20 Future rules are far from perfect (or even mediocre), but there are enough variant and house rules about to make a d20 Trek game a viable option.
mactavish out.
Our country's past progress has been the result, not of the mass mind applying average intelligence to the problems of the day, but of the brilliance and dedication of wise individuals who applied their wisdom to advance the freedom and the material well-being of all of our people.
-Conscience of a Conservative, Barry Goldwater