A leak concerning Pokémon generation 4 shows how different the series could have been. Game Freak was tinkering with the idea of implementing gender differences among a multitude of Pokémon.
Whether or not this leak is accurate is up for debate. However, it does come from Dr. Lava, someone who has a long history of analyzing Nintendo titles. According to Dr. Lava, this leak originated on /VP/, a 4chan forum where anonymous users post about Pokémon prototypes.
On Dec. 19, one user posted images of what looks to be gender differences for several Generation 4 Pokémon sprites.
While there were only a handful of images shared, supposedly, every generation 4 Pokémon was going to feature some gender difference.
The gender difference would exclude Pokémon like Dialga and Palkia, of course, as they are genderless like all legendary pocket monsters.
Some of the differences were minor, such as the female Charizard having one horn instead of two. Others, however, were quite noticeable, as we can see with Wobbuffet and Pikachu above. From the images, it appears that females differed the most from their original male counterparts.
If Game Freak actually went through this, Pokémon would look completely different today. Mega Evolutions would have an entirely new look to them, as Game Freak would have had to account for each gender.
Of course, this is just a leak, so we can’t know for certain if this was actually in development or not. Though, it is interesting to ponder, true or not.