"...downright ignorable..."
By who? Your problem is something that is directed towards a specific group of people, not the community as a whole. Lee is frequently played at higher Elo's because his kit gives him a lot of tools to work with, and the specific players are capable of using it appropriately. At the same time, players at higher Elo's know exactly how to deal with him.
This is not always the case at lower Elo's.
"...extremely bloated, does way too much..."
Compared to who? This comparing two champions to each other, or comparing Lee to some concept that champions ought to fight X mold. That's not the purpose of the game; it's not to create champions who can all do the same things, but rather to create a unique diversity among the champions that allows intricate plays to be made on a game-to-game basis. Compared to Trundle yes, Lee does a lot more; however, the same principle doesn't extend to someone like a LeBlanc or a Zed who can outplay as well. Is outplay unhealthy for the game? Personally, I don't think it is.
"...very, very few weaknesses..."
Ask any player what Lee's weaknesses are, and I'm positive you will have a slew of responses.
- Lee has good early game damage that can be matched by other early game junglers like Elise
- Lee has a lot of skill attached to his kit that requires at least some knowledge of how the kit works to be successful or even average.
- Lee falls off late game into being nothing more than a peel machine and an dive fighter.
- Poor management of your energy and passive = lose
And that's just the few off the top of my head.
So no, I don't think his kit is bloated or unfair in any manner. I think players just need to figure out how to deal with him and learn what they need to do to deal with him.