My theory is, King Koopa is the "good guy" in the Mario games.
This idea stems from a few things. First, Peach, Princess of the Toad Stool people, is human, not a Toadstool. Second, Koopa tends to go for the Princess instead of attacking the Toadstool people directly.
How would a human come to rule over the Toad Stools? Especially in a land with little or no other humans? It is my belief that through bloody combat the Princesses fore-fathers took control of the kingdom. Perhaps the princesses great-grandfather is known as Olaf The Shroom Slayer.
Also, why does Kooda always try to kidnap the Princess? He has over whelming number of troops that are combat trained. Taking the Kingdom should e a piece of cake. It is my thought he is trying to save the lived of innocent Toadstool by avoiding direct combat. I would even guess that the Koopa's were citizens of the kingdom prior to Peach's family taking control of the kingdom. The Koopa's might have even been the former leaders. But it is clear that the Koopa's are trying to remove the human leadership from the land.
Now we have Mario, duped into thinking Koopa is the bad guy, helping keep human tyranny in place.
That is my theory.