It's about a combination of love and mythology.
The iconic, beloved characters get great power. The iconic, not-beloved Vader get almost-great power.
It's weird, but the evil toons from Old Republic (Sith Triumvirate, etc.) may not be as iconic to most people since so many who saw the movies never played KOTOR, but to those who did play the game - and this fanbase is a Star Wars /video gamer fanbase - they spent a lot more time interacting with those characters than they did with the movie characters, and some of them were even playable. In other words, there was more opportunity to grow to love them.
So we EA/CG gives bonus power points to iconic toons, and more bonus power points to well-loved toons, and then more bonus points to toons who come out later in the game (because of power creep), and voila! You have your explanation.