@Andy Willow It's because the entire universe was destroyed at the end of Galaxy 1 & a new universe got rebuilt. Bowser & Jr. are from the old universe while the current Koopalings are new universe & thus not directly connected anymore.
Hey, it's more of an explanation than Nintendo gives.
Not sure if Jo is a little late to the party with this. I've seen some Reddit pages who have been hyping this battle since Sunday.
I was off line Saturday and I'm sure thats still a day late to the reddit party.