Koopa Paratroopa is pretty obvious; it was playable in Double Dash!!. Queen Bee's inclusion is due to the fact that she likely won't be used anywhere else, besides spin-offs now.
Queen Bee is obviously the most available choice of female heavy racer. Despite species problem, maybe the staff don't want to put the Paratroopa and Koopa Troopa players at one time because they look similar, but IMO Paratroopa can be a color-change option of Koopa Troopa.
On a similar manner, In terms of Petey Piranha, I'm quite certain that his huge head is the reason why he hasn't attended any additional Mario Kart titles. After all, that big head of his makes it harder to see what's in front of you.
