Sadly, I don't have a lot to add as I've not actually played any edition of the Star Trek RPGs.
However, from all the gamer Trekkies that I know, they seem to almost universally prefer the version published by Last Unicorn.
I did own the Player's Guide for the version published by Decipher for a short time and it was interesting. Almost a combination of a "d20-like" resolution system (but using 2d6 instead) with the "merit and flaw" type mechanics thrown in a la WoD. It is supposed to be nearly identical system-wise to the Lord of the Rings RPG that Decipher also published. But I never actually played it so I couldn't offer more than speculation.
HARRY DRESDEN — WIZARD
Lost items found. Paranormal Investigations.
Consulting. Advice. Reasonable Rates.
No Love Potions, Endless Purses, or Other Entertainment.