Well, the Jedi masters in the Empire stories do indeed get very little characterization and 90% is also mischaracterization.
In generel you're right, the Sith characters do get better characterization. Some Jedi Masters do have potential, though. Especially Orgus and Braga. But you only see them for one chapter, which is kinda sad.
Also, Jaric Kaedan. I'd love if he had been more important throughout the story. (Guess I'll have to write some fanfic.)
There is also Syo Bakarn. He isn't that interesting, but I still thing when it comes to charecterization he is comparable to Thanaton.
Thanaton is quite annoying and ************, but his character is quite memorable.