I'm not even going to count Noble Six, as while their story was neat, we didn't get much of it at all, thanks to ONI in-game, and out-of-game because Six was basically a self-insert, hence the customization and all that jazz.
1. Jorge. His compassion towards people and his ability to see himself as a human and not just a Spartan struck a chord with me.
2. Jun. His sense of humor did make me smile now and then in what was otherwise a rather grim adventure.
3. Carter. No strong feelings one way or the other. He was professional and did his job, but we didn't get to see much else of his personality through his actions/thoughts. Quite the exit, however.
4. Emile. Always came off to me as brash and overly dark. I'm sorry to say that while this may not be true for all, most individuals I have met who claimed Emile as their favorite tend to be reminiscent of teenagers still in their "edgy black and red" phase.
5. Kat. Blunt to a fault at times, and incredibly standoffish. Worked well for her character considering the tale of the last Noble Six before you and her involvement, but it prevented me from connecting with her as a character at all. Plus she really needs a restraining order placed on her on the behalf of all innocent vehicles. (Also, on a side note, Anthony Carmine had the better headshot death, imo.)