Actually, it is implied that they are seperate in the first two canons R/B and T/D/S, and they actually are seperate in the Gates to Infinity canon.
If that is indeed the case, how do you explain the fact that the protagonist in Explorers of T/D/S is a human from that world? (granted in its future, but still in the same world)
It's one of those loose end things that never gets a proper explanation. We get no real explanation as to why the protagonist exists, but at the same time we get the same implication about the existence of humans in that reality as the first games.
Looking forward to Pokemon X and Y. White FC: 0862-2660-4156 / 3DS FC: 2492-4470-1418 / White 2 FC: 4556-7836-2644