Where any app that wants to change behavior when you get a call must request permission to your IMEI and calling/called number? Or why the broken, upfront, all or nothing model is still even used?"
At the time android created its permissions model, most of these issues were not obvious, or it would have been done differently.
Remember, of course, that prior to things like android (the first version of the iphone only had webapps), permission models of any sort were pretty much unheard of. Flip phones running java apps, or blackberries, had apps that got to do whatever they wanted.
Permissions changes are being slowly made in android. The same way you'd slowly change most serious things about something with billions of users.
It's not like C++ or Java just release new features every day (even if we may want them to :P).
This is of course, the same as any large system in engineering.
I don't know enough to comment on the rest.
" At what point are we allowed to say Google's mindset is not "don't be evil" as far as external observers are concerned? Or will everyone that brings this up always be labeled as unable to understand?"
Truthfully? It doesn't matter. At some point, every company large enough will lose its sheen, and people will worry about it, and eventually question its motives. Nobody can be perfect at doing the right thing all the time, even if they wanted to. Eventually, even with the best of intentions, mistakes add up, and people stop believing. In fact, i'd wager it happens slower if you don't even try to have good intentions, and and just stay under the limelight, rather than try and occasionally mess up.
In any case, I guarantee the same will happen to Mozilla (or whoever we want to peg as the current defender of the world) over time, the same as it has happened in the past to every other company. Non-profitness won't save them.