If we overlook the fact that Pokémon Red/Blue/Green started it all, I would say that the generation 2 games were the greatest.
Two new Pokémon types, type match up adjustments, Pokémon were able to carry items, revisiting the Kanto region, etc. The game brought so much new for the better and kept literally everything that made its prequel so great intact
Not to mention that the first two generations clearly had the superior Pokémon design...