Awesome Music: Former Star Trek: The Next Generation composer Ron Jones, who was unceremoniously axed by executive producer Rick Berman for providing music that was "too noticeable," makes a triumphant return to the franchise with the PC game, and demonstrates what the TV shows were missing.
Polished Port: The 32X version actually did improve on the SNES version in several aspects, including more detailed graphics and a 3D pool minigame. The only major downsides were that it was a lot weaker in the audio department — which was kinda inevitable since even with the 32X's added audio channels the system just couldn't compete with the SNES in that regard — and that the 6-button Genesis controller wasn't quite as suited to the game as the SNES controller (and god help you if you had a 3-button Genesis controller).
The Problem with Licensed Games: Just about averted with the console versions, which aren't regarded as anything overly impressive gameplay-wise, but are decent enough by the standards of both Star Trek games and licensed games in general. Thoroughly averted by the PC version, which is up there with the likes of Elite Force and Interplay's adventure games when it comes to the best Star Trek games.
Scrappy Mechanic: In the SNES and 32X games, failing to take your ship out of Red Alert before you warp back to the starbase will add a not-insignificant penalty to your mission score. Commit this mistake on more than two missions, and it's impossible to get the best ending.