- Baby Bowser is the younger form of the current Bowser, seen in Yoshi's Island, Yoshi's Island DS, Yoshi's Story, and Partners in Time.
- Bowser Jr. is Bowser's eighth child, living in the present, who happens to look a lot like him. He is in Sunshine and Galaxy.
- The multicolored little Bowser-looking things in the Mario Party games, including the one you can play as in a couple of them, are Koopa Kids. (Not to be confused with Koopalings)
There's no overlap between those three categories (other than the fact that Baby Bowser in PiT uses Bowser Jr.'s design instead of Baby Bowser's, due to some apparent confusion on Alphadream's part).
As for the issue of Koopalings getting in the way of original bosses, I would support putting the Koopalings wherever multiple instances of Bowser Jr. would have been placed otherwise (NSMB minibosses, SMG monologuers). That seems like a fair balance for now.