Honestly, I think the hierarchy of the Iokans is more about who is the most able in more ways than not. Ayla would be a prime candidate for pretty much any sort of society, were she adapted to that era's standards. Physically, rationally and philosophically she's superior to pretty much everyone of that era, save Azala, to whom she still outdoes in physical prowess. With just how able she is, it's of little wonder that she's chief; she rules her tribe, and does so for good reason.
Kino, it seems, is able to take notice of things overlooked by most, such as the amount of attention Ayla seems to be giving the three that arrive, especially Crono, who he more than likely perceives as competition as a mate, not just the childish jealousy that it's made out to be in-game. He also managed to take the Gate Key without anyone noticing- given, they were all hammered, but still- so he had some measure of dexterity, not to mention what had to have been distinct cleverness, as displayed in the Tyranno Lair, where he leads a group of humans out of the stronghold with, apparently, nobody getting hurt. To do that in a castle full of dinosaurs would take some brains, not to mention brass balls. Based on that, he would probably have ended up becoming the next chief, even if Ayla hadn't connected with him as she did. Though in comparison to Ayla he may have been a weakling- then again, the only one on your team, and probably in the entire world, who isn't just that is Crono- he was by no means incapable. Therefore, it would make sense that Ayla would have said that he was to rule if she died at some point, since she trusted him and his abilities to lead the Iokans.
