This is a paper doll game, not a tool for making RMXP-compatible sprites.
The positioning of the Pokémon around the trainer seems rather off, for example:
Vaporeon is the worst offender of stealing the left-hand Pokémon's glory, although it's likely that many of the Pokémon in all three positions could stand to be moved around a bit (I've not tested most of them). The right-hand Pokémon should probably be shown behind the middle one. I'm not sure about the relative sizes of them all either.
The first Eyes option doesn't work for the male version.
The hair antenna is very much in the wrong place (both male and female), and shows up through hats (some "hats" should allow it to be shown, though, depending on the styles of the hat and antenna).
Might it be a bit clearer to have the "none" option as another of the big boxes to choose from (put it first, not last), rather than a separate small icon in the bottom right?