I'm a little confused here. You want to ban things based on usage because they make other pokemon unviable. Banning things on usage makes zero sense because they if you continously ban let's say the top 3 pokemon in OU just because they are the most used you end up banning every single pokemon. IMO this is the wrong way to go about the metagame.
I believe that the bans should be kept simple instead of doing complex bans. Complex bans opens up this whole argument of let's bring down ubers but they can only be at lv50 or they cannot be EV'd. That doesn't make any sense, and I think it would be best to stay away from that sort of a scenario.
But then again there was the SwSw+Drizzle ban. While I know that it probably won't be repealed anytime soon, I think it would be better to perhaps individual test Swift Swimmers or just ban the ability upright. Of course my opinion doesn't mean much but it's just what I believe.
I think the question that needs to be figured out is what defines a uber. I think that the best definition is the Portrait of an Uber thread which gives a good, comprehensive definition of what makes an Uber. While the thread was over 2 and a half years ago I don't see why it still can't apply today.
I'm not saying just start down the list slowly banning everything. I'm saying every month, ban the top three in usage for the next month, and bring down the three banned the previous month. This allows us to see how removing certain pokemon affects the metagame, and whether the metagame would be better off without them. Currently, there's no way of knowing.