Why do so many counterpart pokemon (frillish/jellicent, basculin, shellos/gastrodon, latios & latias, sawk & throh) seem to divide into blue and red specifically? (Also, did people model gendered fashion off of jellicent, or did they get bred so males had mustaches and females had lips and eyelashes?)

Coincidence.

That may sound like I’m being facetious, but there have been a number of studies on this point, all of which came to this exact conclusion.

The same could be said in response to your question concerning jellicent. Jellicent simply evolved to look like that on their own, and human concepts of gendered fashion just happened to mirror the jellicent through a completely unconnected (to the jellicent, that is) series of cultural shifts. It’s quite fascinating, really.