Do you know what is worse than people deriding the lack of FemMC in the extended canon? People trying to impose those opinions/views onto others.
Truth be told, both routes are perfectly valid, though I do tend to agree with the game's suggestion of going for the male route first. It is, for all intents and purposes, canon - meaning you'll encounter that version of events in all extended media. It may cause a little bit of confusion later, if you choose to go the other route; though that also assumes you'll want to play it again, and that you'll stick around for everything else. It's the 'intended' experience, whatever sway that holds over you.
The female route carries a lot of affection for most (me included), precisely because it builds upon on what you already know. By the point of P3P's release, fans were already well-aware of established character relationships and quirks, so it especially novel to see all that turned on its head, and being allowed as the player avatar, to approach these personalities on completely different terms. I think a lot of the fun of this route, comes from the subversion that takes place.
You can't really make a wrong choice - it's just that there are caveats to each!