Hmm, this is tough. I didn't and still don't actively dislike any of the Anis, although I do find some of them more compelling than others. All of them were necessary to the fight and I seriously believe that had any of them died during the course of the books, it would have been game over.
Marco: I pretty much love everything about him. Including (and possibly because of) his mean/ruthless streak. I liked how he brought levity to even the darkest situations. Out of all of them, Marco had the strongest (IMO) reason for not wanting to fight - but he did anyway, which is really brave. I thought and still think that out of all the Animorphs, Marco received the best treatment in terms of character development and I always looked forward to his books, poo always seemed to hit the fan when it was his turn in the rotation, LOL.
Cassie: Despite being so different from Marco, I thought they were two sides of the same coin. Cassie had a real mean/manipulative streak and I thought that was an interesting contrast to her predominantly compassionate nature. I'd argue that she was the unofficial second in command...in retrospect especially, it's quite apparent how much Jake relied on her opinion and looked to her before deciding whether or not to go through w/ something. I also appreciated how she continued to fight despite being a pacifist...her moralizing got extremely grating and frankly, she was hard to like towards the end of the series, but at the same time, I blame the ghostwriters for dropping the ball on her character. In the first half of the series Cassie was a lot more humorous, and wasn't nearly as self-righteous. I always thought it was cool how she'd often be the one to come up with the plans despite not wanting to fight in the first place (just like Marco).
Jake: I know a lot of fans found him boring but I couldn't disagree more. I think Jake was an amazing character, from the beginning to the end of the series. Here you have this regular kid with what seems like the picture perfect life, when in actuality he's basically in a living nightmare: his brother is a slave, his parents are totally oblivious, and the fate of the Earth (possibly the universe) is on his shoulders. Out of all the Anis, Jake was the biggest wildcard, IMO. He was the least predictable in terms of his decision-making...just when you think he'd go one way, he'd decide on something completely different, which was realistic considering the evolution of his character. On an emotional note, I liked that despite being chosen unanimously as the leader, he was so deeply insecure, which was most apparent during his own narrations. The Jake books were not always as action packed but they always made me wonder how the hell he'd be able to live a normal life if he survived the war. I guess we all saw how that turned out.
Ax: I like Ax a LOT, especially earlier in the series, but to be honest, I didn't make a huge effort to get a hold of his books later in the series. I loved reading about the world through his eyes and I appreciated how he philosophical he got when it came to the heavier issues. His viewpoints really made me think.
Rachel: At the beginning, Rachel was probably my favorite, but like Cassie, I think her character suffered greatly at the hands of the ghostwriters. Just like Cassie's over the top moralizing, Rachel's violent nature got way too hamfisted for me. Rachel was definitely the bravest, but IMO, it was never b/c she was blindly reckless. The ghostwriters disagreed with that apparently, which is why I often found myself rolling my eyes at some of the truly stupid risks Rachel would take. I just think she lost most of her complexity by the time the last few books came around.
Tobias: I know he's last on my list, but I don't hate him at all. I just don't think he's nearly as interesting as so many fans find him, heheh. On paper, his story is probably the most interesting, his character just never really struck a chord with me. Maybe it's b/c I couldn't relate to him being bullied, the outsider, etc...his narration was frequently too emo for my tastes. I did find myself agreeing with him a lot when they would all debate whether or not a certain tactic would be justified. He was like the perfect balance between Marco and Cassie in that way.
tl;dr I know. I seem to have a lot of feeling on this topic.