There are two reasons for this, the first one regards the starters. They have a higher male ratio to make them more difficult to breed early on in the games, which was done on purpose. This is also true for other Pokemon like Combee, for example, since only the female can evolve into Vespiquen and they wanted that to be more difficult for players to obtain.]
The second reason is cultural. The anime is shown in many countries, but the Japanese are their main public. They try to be as diverse as possible to reach a wide demographic, but some things remain for particular audiences. That said, in Japan it is very normal for men to dress like women, be androgynous, and things like that. They also mimic this through animes and games, in terms of games "The King of Fighters" is a good example.
In a country with such a different culture from our own, this may look strange, but for other countries it not only looks normal, but also cool. The developers of those animes and games are professional people who understand that some people only like certain Pokemon or characters because of their appearance, so they try their best to be diverse and appeal to as many people as they can.
(Some pokémons could be only female like Jynx, but they do this on purpose.)
[Just by curiosity Gothtelle has higher female ratio and Gardevoir equal male/female ratio]