Gender ratios with 87.5% male chance (all starters, fossils, eevees, etc.) exist, as some people have already said, to prevent players from "over-breeding" pokémon that are intended by the game to be both rare and valuable: I guess gamefreak thinks a player just tossing its starter after its 30th child is born with better IVs defeats the point of bonding with the pokémon and all.
All other gender ratios outside of this one and the classic 50%-50% exist mostly for flavor.

Breeding mechanics aside, people have so many different interpretations of how "gendered" a pokémon looks that I think it is just a matter of personal interpretation and should not apply to anyone else other than the person who sees it that way. For example, I tend to see Goodra and Gardevoir as female, but I would find it stupid that they were made into 100% female species just because they look that way to me.