I can definitely see it, though I've only read Sower so my view's incomplete. There's some lip service paid by her dad early on about her needing to learn humility which def rings true, but I don't think much comes of that nor does it present much a problem, it kinda just gets softened when she acknowledges that she'll be trying to learn from everyone. Same with her mercenary nature when she Harry and Zara start their road trip, Harry's rightfully unnerved by how different she is from how she presented herself before, but then she just starts softening up. Thoigh to an extent she can kinda control her hyperempathy: if she's not looking at the hurt she doesn't have to feel it.

I think there's something of a wish fulfillment element in her; a lotta folks feel at times that things are gonna go bad and that they're among the few willing to acknowledge it, I reckon that part resonates strongly.

I dunno, I liked her. So often "good" characters in fiction end up willfully ignorant, and I find it refreshing when good is not soft or dumb, haha, which I felt she hit well. Plus she seemed humble in some ways to me, like deferring to Zara, confident in the stuff she could back up. And Earthseed resonated with me.

EDIT: I can also see her frankness as potentially coming across as abrasive, but I do also wonder if that and her confidence/arrogance would be seen as less unlikable in a male protagonist, haha. Gender can definitely be a factor in mary sue discourse/judgements.