I probably won't do it myself, but it shouldn't be too hard to change! just create 2 new onion objects with assorted pikmin objects of different colors. Also, I guess you'll also need to add hazards in the world which respond to different types of pikmin :p
Please do keep me updated on how you remake this game, and send me a link when it's done :)
Also unrelated: here's a discord server you can join to share what you've made: https://discord.gg/ggqZ2c4