D6 Star Wars, Revised & Expanded, has still got my vote for best rpg rules married to a setting--it's simply one of the best out-of-the-box rpgs I've ever seen.
There are different versions of Star Trek. I love the universe. It's a perfect set-up for an RPG, especially if you play in the Classic Trek time period of the original series. The players play the department heads on a Star Fleet vessel. It doesn't have to be a Constitution class. The smaller ships are quite fun to play, too.
The GM is free to throw all sorts of weird stuff at the players. Anything goes. This can be some wild science fiction.
If you want to run a simple space battle or planetary encounter with the Klingons, then, no problem.
If you want to describe a giant human hand made of hydrogen atoms that reaches out and grabs the ship....again, no problem. The universe will handle that kind of adventure. More than handle it...welcome it.
From personal RPG stories that focus on a crew member being a detective while he's not on duty, trying to find out who stole his bavarian cookies his mother sent him from Earth--and adventure that takes place entirely on the ship...
...to an RPG story that has the crew visiting pocket universes, other galaxies, or time travelling forward or backwards on Earth, Vulcan, or other worlds...
....Star Trek can handle it.
It's a fantastic universe for a rpg group to explore.
FASA's Star Trek rules are quite simple. Percentage based. Roll skill or lower to succeed.
And, FASA has a brilliant space battle system designed for role playing space battles on the bridge of a ship, allowing players to man the various positions on the bridge.
Fantastic game. Simple to learn. Easy to play. And, it's very interesting with a creative GM who knows how to tell a good story.