QBR and QB Rating have their good and bad.
QBR is like a baseball stat that places more emphasis on "not striking out" as opposed to how many hits you get. Sure, the "not striking out" might give a good indication of your plate discipline, but does it really say how good of a hitter you are?
The more I see the numbers, the more I am actually starting to lean towards QB rating as a better indicator (most of the time). I feel like there are too many subjective metrics in QBR, disguised as "objective". For instance, 3rd down success; do we punish a QB for throwing a ball away in the face of pressure and no open WRs? How about in a tight game, hanging in the pocket to try to make a play only to get sacked?
I feel like QBR rewards QBs for taking the uber-conservative route over actually making plays. I am not trying to say that QBR is worthless, but I saw Kaepernick do little to nothing except "not screw up" and get a 99 QBR, while having a 90 QB rating. Should a QB really be given a perfect score when going 10-16 for 150 yards in a blowout win? Yes, that is efficient, but that's also like saying you won the spelling bee by spelling the word "dog" correctly.
Here's a pretty simple rule in judging QBs in my opinion, trust what your eyes see and brain tells you. Fantasy sports have ruined how we judge players nowadays because we rely on the box score and numbers, over watching a game and judging a performance based on the actual circumstances. A box score doesn't care if you are on the raod or are missing O-lineman.