I think if anything it would/should be Marco. He has a mind that's relatively cool under pressure/stress, and he has the strategic approach. If you want to win a war you have to be able to think about everything in a pragmatic fashion, or else you're going to get into situations you can't get yourself out of, like Rachel seemed to do at times. Marco also had the ability to look at everything objectively, which seems like the rest of the others had a hard time doing. He was willing to do what it took to win, even if it meant killing his own mother, and that just demonstrates that he could be counted on to make an informed, logical decision no matter what.
I wouldn't go so far to say that Rachel was "ruthless," but she definitely didn't always think before she did things. She was more of a "tell me what to do and I'll do it no matter what," type of person, which is valuable, but things never really go well when she calls the shots. There were numerous times when Jake went down she took charge immediately after, and she didn't always make intelligent moves. I think in MM3 when Jake got shot she told Ax to go and kill the people who did it, which was really dangerous to Ax and it didn't help the mission at all (they should have been going after V4, not the people in the battle.) I think in the last book in the David trilogy Rachel did something similar, which split the group up and left her vulnerable to David. And of course, there's book 37...but I hesitate to really quote any of that because the book was just not that great on a lot of levels. -_-
While Ax seems like a good candidate because of his knowledge/military training, I don't think he'd really be able to thrive in a leadership position (at least on earth) for a lot of reasons. Firstly, he doesn't know enough about earth to lead a guerrilla group. If it were a straight up attack force, maybe, but since they have to blend in and hide in a lot of places, he wouldn't know what the best morphs were for each place/job. And an Andalite leading humans is just asking for a lot of values dissonance in the group (what do you mean don't just blow it up?!). I think Ax had the right idea, when in Rome act as the Romans do and just let the humans handle their own invasion.
Though on top of that, I think Ax had a really big insecure streak too, which would make him undermine himself in a leadership position. He always seemed to feel as though he needed to be led (which was part of his training,) but on top of that he seemed to just crumble down when he was put on the spot to make decisions at times. There was a lot of that in 18, even though he was basically dealing with a lot of hostility directed towards him, part of being a leader is dealing with decisions that screw up and make a lot of people mad. But he also didn't trust his own judgment enough, like in MM3 when he noticed something was wrong about the troops that came and killed Jake, but he didn't press the issue when someone told him it was okay.
As for Cassie, I think if she were second in command they'd be so careful and moral they'd never get anything done. Though at times in the book I wonder if she was really the second in command. I wonder how much influence she had over Jake's decisions. I don't know if this is correct, but it seemed like towards the end part of what caused their relationship to crumble was the fact that Jake just started to disregard her opinions, and she wasn't able to handle that.
