I have to say RBY. It laid the groundwork for the metagame we know today, and yes, it wasn't perfect, and yes it was Psychic-dominated (which of course today, we simply cannot fathom), but it was a start. Of course, later generations built on it, as we've already seen.
GSC gave us the Dark and Steel types, Hidden Power, Leftovers, many common Pokemon in today's metagame, like Tyranitar, Blissey, Skarmory, Heracross, Kingdra, and Celebi. It also gave us breeding, and egg moves, which added a whole new layer of strategy to raising your competitive squad. Interestingly, Magneton gained the Steel Type in the generation shift, making it the only fully evolved Pokemon to change types in this way. Crystal also gave us the first Move Tutor, who gave those without access to RBY Thunderbolt, Flamethrower, and Ice Beam. And there's something else everyone seems to have forgotten - the revamping of critical hits. No longer was it based on speed, now, every move had a set critical hit ratio. This caused a huge fall from grace for Persian and Dugtrio. Finally, weather moves and Spikes. Rapid Spin was now no longer completely useless!
RSE's most important change, though not the most obvious, was the EV Cap. No longer could you EV even the frailest sweeper with 252 EVs in HP and Defences. Now, you had to actually figure out what you needed to KO, what you needed to outspeed, and what you needed to survive. And then combine them all. Next, abilities! No longer was Gengar vulnerable to Earthquake, you thought twice about statusing Espeon, and Dugtrio became a revenge killing machine. Natures added another level of strategy, you had to ask if you wanted power, or speed. Salamence, arguably the most dominant Pokemon throughout the whole DPPt metagame was introduced, as were Metagross, Jirachi, Swampert, and Flygon, as were many others. Choice Band and pinch berries were also introduced, and more Move Tutors appeared, making the deadly Explosion available to many more Pokemon.
And now, DPPt. Oh my. The physical-special split, Stealth Rock, Garchomp getting banned, more awesome abilities, notably Technician, which turned Scizor into the bastard we all know and love in today's metagame, MORE Move Tutors, Choice Specs, Choice Scarf, Life Orb, Focus Sash, Toxic Spikes, which gave stall another weapon, type-resist berries, and, most crucially, Wi-Fi. No longer does everyone have to use Shoddy or Netbattle. The Battle Recorder now lets players see where they went wrong, and allow them to learn from their mistakes.
In short, RBY laid the framework, and that's why I feel it's most important. That said, each generation had slowly improved on it, and shaped the metagame into the thing it is today. Scizor, once pretty useless in GSC, sits at the top of the tree. Salamence, though weakened by Stealth Rock, is still an incredibly prevalent threat. You can now no longer be certain what item a Pokemon is holding as soon as it's sent out. Someone used Starmie as an example,saying it used to only hold Lefties. Now, it can run so many items, it's insane.