I love them all so much. I picked Rachel as my favorite, but asking me to actually order them the way the rest of you have been... yeah, it's just not going to happen. My thoughts here have been rearranged into the order in which they first narrated their books-
As a kid reading the series, I never found Jake remarkably interesting. He spent most of his narratives wondering about his decisions, and to me, leading has always been something you just do, more than something you overthink. Reading the series now, I really appreciate him a lot more, though. I feel his strength and the confidence he gave the team got them through more situations than I can count, and I have more interest in his thought process than I used to. His interest in the military that seems to have been nurtured by the war is something I always thought was kinda cool, and wish they would have commented on just a few more times throughout the series.
I absolutely love Rachel during the first half or so of the series. She's brave, and increasingly ruthless and reckless, but still very intelligent with a great sense of humor (a lot of my favorite conversations in the series consist of the early-books banter between her and Marco- she's awesomely witty). During the later half of the series, her character got so messed up and so smashed down to one dimension, I can't honestly say I liked her much anymore... sad day, but I feel like Rachel's "Rachel" got lost in the mix somewhere.
I always liked Tobias, and he never really came across as super-whiny to me. I dunno. I guess I could sympathize with his angstyness to a certain degree, but there's more to his personality, and honestly, I really liked him for the most part. He had a few moments that really bugged me (falling to the ground and freaking out for like an hour mid-battle when he realized his cousin was Visser 3 in disguise) but I admired his ability to keep fighting and keep moving forward through all the **** the series threw his way. Is some sympathy for his angst a requirement for liking his character, maybe?
When I've read the series, I've never really seen any reason to dislike Cassie. I never really liked her all that much as a kid, but now, I admire her bravery and willingness to always, always stand up for what she believed was right. That's not a remarkably easy thing to do. I can see why a lot of people don't like her, but to me, she was a wonderful contrast to... basically all the others in that regard. It does really bug me, however, that she decided in book 9 that she was willing to do what she had to in order to defeat the Yeerks, and yet her moral dilemmas continue after that as if it'd never happened- she never even thinks about it again. It may be people like Marco and Rachel who win wars, but there can't be peace without a few Cassies around.
Marco's an incredible character to me. He's complex and emotionally very deep, but at the same time, he hides it well, and he's always looking at things logically to try to figure out how to win. I'm a lot like all the Animorphs in certain ways, but I'm probably closest in personality to Marco, not least of all because of his sense of humor and his outlook that it's better to laugh than cry. I really respect his strategic mind, and how well he held it together throughout the war. I think his sense of humor got a bit screwed up in some of the ghostwritten books, though.
Ax was always my favorite as a kid. I think I just liked seeing someone almost as socially awkward as I was. Plus, y'know... aliens are cool! These days, reading through the series, I got a bit sick of the fact that every single one of his narratives seemed to deal with his loyalty to the Animorphs. Like Cassie's reason for fighting, it seems like it's just a string that he never gets ahold of in spite of multiple narratives about it. If he'd actually learned a lesson and maybe developed a little as a character, he'd have been more interesting to me. Still watching him struggle with human culture was always a joy, and the stories about what he was like back at the academy ("I wasn't paying attention that day... and there was this female...") never fail to make me smile. I really wish we'd gotten more information on him throughout the series.
Too much? I likes my Animorphs...