So how come Giovanni had lower level Pokemon that got progressively stronger after each time you battled him ?

It doesn't really make sense that the Pokemon he used were the same pokemon that made him a gym leader when they aren't higher levels until later in the game.

and if they weren't the same Pokemon, then what stopped him from using his more powerful ones throughout the game?

I feel like Giovanni should have been some sort of secret boss mission, and he is hidden in hideouts throughout the game, and you need to take him out each time.

Thoughts?