For me, I like how we can customize our toons and our bridge officers (although I still think Bolians should be allowed to have hair) and I ABSOLUTELY LOVE the visual display of Tykon's Rift!!!
What are yours?
For me, the only real thing the game needs to make it perfect is just more content.
What I love most about STO
1. Graphics: Simply put, this Cryptic Engine looks and runs beautiful, this is definitely my favorite MMO engine except for the instancing.
2. Music: Not too many MMOs out there have music you'll want to listen to outside of the MMO and the music does just so much in drawing you into the game.
3. Customization: As you mentioned, the ability sincerely customize our own officers as well as make our own aliens is simply awesome! Now if only we could apply half that customization capacity to our ships!
4. General: I've never seen an MMO run so well outside of release, it's phenomenal and would have been perfect except for the lack of content.
5. Some episodes such as City on the Edge of Never and Premptive Strike were just plain fun. I want to see 5x the amount of missions like that.