I like the idea, but you're missing one major part of this that will eventually lead to it not working. That is, whats in it for the carriers. You make some great points, but you are just assuming these things will work. Show them in terms of monetary value why this will work. In the end, if we want this, we will have to pay, and we are all going to be willing to do that.
So... What are my ideas? Don't have special phones for rooters. Have it the ability of EVERY phone to be rooted. Have that rooting app, or kill switch for the lock a pay service. You want to root? Sure, but pay $5 or $10 to do it. Boom, thats $5-$10m in revenue to the carriers and manufacturers for little to no effort on their part. You want to remove some of those bloatware apps? Sure, the OS will allow you to do that... For $1 per removed app. You want to run a custom ROM. Sure, make a ROM & Theme Market for them. And set aside a percentage of those purchases for the carriers and manufacturers. They get millions more in their pockets, and suddenly the ROM developers are making money as well.
Present it like that, and you might get somewhere. Present them with hard, tangible numbers and they'll listen. Yeah, it will suck that we will have to pay for this, but in the end, it would be more than worth it, and would take Android to the levels we know it can be.