If you're making a fan game, and you want to do something creative and different, why not change stuff?
It's your game, and like Yami said, as long as it works for the player it shouldn't matter what you tweaked, it's like in performing arts - The public doesn't know what you're doing or how you did it, they just see the result and judge if they like it or not based on that. If you think those changes work and make the game a better experience and you enjoy them, then by all means you should do it!
(By the way, i'm very interested about your Four Star Mon game. Where can i see it? Looks like an interesting idea!:D)