Definitely Jake--always was, and always will be. I always liked him the most when I was reading the books--I liked his personality, his situation, his relationship with Cassie, etc, and his utterly tragic arc at the end just made me feel for the guy and be interested in him all the more. I remember when getting a MM2 book for example I specifically wanted the Jake one, since he was my favorite character. I even had a little crush on him back then!
After Jake, the order of characters is more tricky, though it'd probably Cassie, Ax, Tobias, Marco, Rachel. Cassie I could identify most with I think, and J/C was my OTP of the series, and I loved Ax and Marco's humor, even if they (especially Marco) could be annoying at times. As for Rachel, I just never was all that interested in her character--her belligerence irritated me a lot as well, and I could never identify all that much with her. *shrug* Though really even Rachel I still like, just not as much as the others....
If David is to be included he'd come DEAD last, I could never stand him, and hated that whole trilogy!
Especially at the end when I still feel he sent Rachel in to die strictly for his own personal vendetta against the yeerk in Tom's head. I hold that against him
I don't think so--he did it because it was necessary. They couldn't let the Blade ship get away and conquer new races, as Cassie pointed out--not in good conscience. They were too dangerous, and they didn't know Erek would do what he did. So yeah, it was poorly planned and executed perhaps, but it was part of important strategy, not vengeance--after all, he was killing his brother as well, which I don't think he'd do just to get revenge on the Yeerk within his head....