What if each new generation of Pokemon games were prequels to the generation before it. Think about that for a second...in gen 1 there are only 151 Pokemon but gen 2 has 100 more? How did we get to 700+ without them knowing about all the other Pokemon that long ago.
If you go back from gen 6, Pokemon have been dying out between each games and we are left with the "original 151"... But then they really aren't the original...just the ones that survived. All the "new" Pokemon introduced in each generation actually died off and left what we know in RBY
Now, if you are thinking "hey, why do we fight Red in GSC then?", there is a perfectly good explanation. Since gen 2 would be a prequel to gen 1...then that means the Red in gen 2 is older than the Red in gen 1...right? Which means the Red in gen 2 is actually gen 1 Red's dad. Remember how in gen 1 he wasn't there at all? This totally explains it. You end up becoming a Pokemon Master just like him.
Also, don't bring remakes into this. I am talking about RBY/GSC/RS/DPPt/BWB2W2/XY...no remakes in this at all.