My theory is that, just like people in our world poach animals for certain aspects they have (example: poaching elephants for their ivory), humans in the mario-verse naturally posess some sort of precious commodity. For a while, the other species in the Mario-verse co-existed with the humans, until Morton Sr. (who I believe is Bowser's father) decided to go on a massive human killing campaign to get this commodity. Heck, even Peach's family was killed (Toadsworth managed to hide Peach so the Koopas wouldn't find her)! That's why Mario's parents decided to leave them on Earth when they were toddlers: to get them away from the killing so they could have a chance at life (Morton Sr. was still king at the time. Bowser was only 5 yrs. old and a prince back then and hadn't ascended into power) Later, when Morton Sr. died, Bowser took over as king and decided that killing the humans was a waste of time and money and stopped the poaching, but at this point, the human race was endangered and spread out across the globe. Plus, human poachers, while not as widespread, were still around, so it looked as though the humans would never get a chance to peacefully repopulate.
Decades later, when Mario and Luigi came to the Mushroom World via warp pipe, Mario discovered the danger that the human race was in, so opened up Mario World (which is from SML2), an island out on the sea, one where no poachers would find, as a Human haven where the human race could finally live at peace
That's just my theory.