And Team Rocket was in the game a lot... a few in Mt. Moon, one guy on Nugget Bridge, some guy standing outside a house in Cerulean City that the guy just stole a TM from, Silph Co., the tower, the casino, the destroyed Cinnabar Lab, not to mention that the Viridian City gym was run by Giovanni.
Nugget Bridge was run by Team Rocket, too. Remember, the sprite didn't look like a ROCKET when you approached him, and instead of giving quips on how they need to catch better Pokémon, or whatever, they all say some variation of "I have done my best, I have no regrets!"