I still think our best option at arch villian should be a version of yourself.
1) Mirror force version of you, similar in every way, skills, traits etc.
2) A Borg version of you guessed it, yourself. Retaining human/klingon traits but serving the collective.
For both of these, im not going to claim to know anything about coding but. Couldnt you just use a code that instead of showing a pre-made character, uses a code to pull your captains image out of the server o.O. Then some code to alter costume designs to go over yours. Like borg implants or mirror force uniform.
The problem isn't just lack of a major villain, it's lack of important characters in general. You don't really make any connections with any characters throughout the game.
The major thing lacking in the storyline missions are memorable recurring characters. Star Trek was about characters, not just flying around in ships. And while the player's character will always play a large role in resolving problems, they should still get help/hindrance from memorable NPCs.