My favorite levels are:
Liberation of Gerrard V
Prisons of Kessel
Liberation of Gerrard V because there is so much action going on, and so many things needed to be taken out. I had to try about five times to get rid of the huge gun turret, that gets me almost every time now! The TIE Interceptors of the 128th are cool as well, I love chasing them down, it's a real challenge.
Prisons of Kessel, same reason, a lot going on, and a lot to take out, there always seems to be more eyeballs to take out, and the squints are tough as well.