I hope Kubiak doesn't call games like Kyle

This is such a good point. Who are the all time great QBs who played in bad systems? To me they work in tandem. A great system accentuates the strengths of a great QB. Off the top of my head I can't think of a great QB who was in a system that was just awful.
I tried to think of a great QB that succeeded in an awful system or played for a horrible team and I can't think of any. It is easier to find QBs who have left horrible teams/organizations/coaches and thrived at their next location than you can those who had to play through crap

Archie Manning.

I honestly don't know if that is true, but lots of older folks in my family swear he would have been one of the greats had he not played on terrible teams in New Orleans. And that's coming from an LSU family that hated to give any credit to an Ole Miss player. I'm just old enough to remember him playing in 1980 and when he went to Houston, but I can't say I knew enough at that age to know if he was good or not.
Just from the limited games that I saw on tape, I believe the he could have been one of the best but as you pointed out, terrible teams usually drowns greatness. Most of the successful QBs usually had stable coaching, a proven scheme, a winning culture, and a chance to develop.