The Koopa Kids were going to be the bosses in Super Princess Peach on the DS, but Nintendo decided against using them. The sprites of them are still in the spare space in the game cartridge.
As for Morton Jr.'s name, another theory is that some relative (probably father or brother) of Bowser's is the original Morton.
Besides where they are now, there's still the question of where they came from. How does Bowser, a single guy who's never had any on-screen romance besides unrequieted love for Peach, end up with 8 children anyway?