Simply go into the Graphics/Picutres/Pokedex folder. All of the files are there. Simply change the colors, assets and stuff using an art program like Photoshop or Aseprite. If you have Graphical Design/Pixel Art experience, this part should be simple.
Just keep messing around with it until you find a style you like. Be sure to keep locations of things in the same place, unless you want to edit the scripts and stuff, otherwise it'll look weird.