Hmm, for me it had to be Marco and Tobias right at the top. Two characters that had great insights and actually developed through the series in a positive way. I think that the ghostwritten books are a tick weaker (okay, more than that for some of them) then K.A's stuff, but Tobias's shift after his torture in #33 made him an even more appealing as a character. In all honesty, despite what he said in #37 ("I'm no ones leader"), he could, in my mind, have led the animorphs. Especially after facing his demons (read: Taylor) in #43, he became one of the strongest in the group. He was the closest to Ax, which made everyone's favorite alien more a part of the group. He sacrificed more for the fight, and he just about always took it without a complaint. Jake, on the other hand, took two big hits (I'm not really counting the burden of leadership here, though maybe I should) and it near wrecked him. How he was in the Hork-Bajir valley, especially in comparison to Tobias (who, to be fair, had just regained some semblance of family) just seemed selfish and brooding.
Anywho, after that long diatribe, I'll deal with why Marco is awesome in my mind. Cool and ruthless, Marco always made the smart call, if not the emotional one (minus that thing where he saved his dad). He too took every hit thrown at him, complained the whole time, but never really broke from it. In fact, minus Rachel, who just ignored the damage she took, Marco probably took the most abuse and kept on ticking. Holding his guts in while cramming the door shut on the Sea Blade in #39, the injuries he took while saving Tobias in #33, fist through the glass with the Pemalite crystal in #10, everything like that just kind of overshadows what some people see as excessive complaining. He was tough and gutsy, and usually ended up with the most pivotal assignments from Jake.
So, to finish the diatribe, for me it goes:
Marco-Tobias
Jake
Ax
Rachel
Cassie
