I think I may have an explanation for the Koopa Troopas' evolution sequence and the Goombas. In SMW2, the KTs were evolved, but when their master, Bowser, had fully grown, that stupid movie was somewhat right about the Devolving ray. Bowser had devolved the Koopa Troopas to a point where they walked on all fours. They were known as shell creepers, or something like that, on MB. Anyways, about the Goombas. Bowser captured some mushroom people that were betraying Princess Toadstool, and used his 'devolving ray' and they became the Goombas that usually die of head damage.
What I don't really get is how a character who doesn't really look like a regular koopa is known as 'Koopa' in Japan.