[CTcard]

... Shaw's system doesn't produce impressive numbers for QB's (even Luck).

That depends how you count.
On efficiency metrics there is certainly no reason Stanford QBs cannot have very good numbers. Most of the time they have had good efficiency numbers. 

Under Shaw we have had:
2011 Luck PER=169.7  1st in Pac 12, 5th in Div. 1
2012 Hogan PER=147.9  4th in Pac 12, 26th in Div. 1 (had he qualified)
2012 Nunes PER=119.6  10th in Pac 12, 85th in Div. 1 (had he qualified)
2013 Hogan PER=151.6  4th in Pac 12, 21st in Div. 1
2014 Hogan PER=145.8  5th in Pac 12, 25th in Div. 1
2015 Hogan PER=171.0  2nd in Pac 12, 4th in Div. 1 (Stanford all time record)
2016 Burns PER=122.6  11th in Pac12, 86th in Div. 1 
2016 Chryst PER=78.4  behind everyone who qualifies

While some of the solutions proposed here are not helpful or practical, and very much the offensive problems are widely spread, one shouldn't counter by pretending there isn't a QB problem.

[CTcard]

... Shaw's system doesn't produce impressive numbers for QB's (even Luck).

That depends how you count.
On efficiency metrics there is certainly no reason Stanford QBs cannot have very good numbers. Most of the time they have had good efficiency numbers. 

Under Shaw we have had:
2011 Luck PER=169.7  1st in Pac 12, 5th in Div. 1
2012 Hogan PER=147.9  4th in Pac 12, 26th in Div. 1 (had he qualified)
2012 Nunes PER=119.6  10th in Pac 12, 85th in Div. 1 (had he qualified)
2013 Hogan PER=151.6  4th in Pac 12, 21st in Div. 1
2014 Hogan PER=145.8  5th in Pac 12, 25th in Div. 1
2015 Hogan PER=171.0  2nd in Pac 12, 4th in Div. 1 (Stanford all time record)
2016 Burns PER=122.6  11th in Pac12, 86th in Div. 1 
2016 Chryst PER=78.4  behind everyone who qualifies

While some of the solutions proposed here are not helpful or practical, and very much the offensive problems are widely spread, one shouldn't counter by pretending there isn't a QB problem.