I agree with you sage.
In games this complexity comes from balance vs design.
The game is designed in a way, works well, then content is added. Some of this content is poorly thought and does not work well with the initial design of the game, so it is balanced with stats adjustments.
The truth is some content simply cannot work correctly in the game, but they can't remove it. Sure with numbers it's possible to patch it so it doesn't break everything, but it's still bad design : ex : short circuit, quick fix, darwin shield, pyro hitreg, natascha, etc..
Another problem is the way valve decides what to do with the game. Nobody knows what they plan to do and nobody understands why they do things the way they do. But some other game developpers have neat systems :
in starcraft 2, before every patch a balance test map is published alongside with the changes they want to make, so players can give feedback BEFORE the actual patch.
in eve online, every year a council of players is elected from every part of the playerbase (miners, PVPers, mission runners, traders, etc) and gets to discuss in detail with the devs about what to do in future updates, what are the interests of the people they represent, and the current state of the game.
I would like valve to use both of these things to avoid all these shitstorms after every balance attempt : publish the changes you want to make early, explain your reasonings, and select a few players from every community (pubs, reddit, steam forums, tftv) to discuss directly with.