Double-checking on bulbapedia, it looks like you're exactly where the game wants you. Which means that Team Rocket really are weaksauce on purpose, I guess?

I always thought this was just wonky game balance, but now I'm more inclined to believe that it's intentional storytelling through game design? Either that or they changed their mind on where the Radio Tower should be in the plot and added the executives later?

Whatever the case, stomping Team Rocket into the dust is funny.