I don't think we overrate Kyoto at all, it's just that if a Japan trip includes Tokyo (and what first Japan trip doesn't?) then Osaka is just another large city while Kyoto actually has a portion that is reasonably different from Tokyo.

Regarding Osaka's location: When I stayed in Osaka while having a JR pass, I got a bit tired of always having to shuttle over to shin-Osaka. If you have thae JR pass, Kyoto to shin-Osaka isn't that much longer than the shuttle.