Given the obstacles I think he has done well. But if we follow your argument then the defense must be put into play, and then there is that pesky dilemma at quarterback. I don't know what the evolution in run/pass QBs has been with the popularity of the shotgun spread, but my gut feeling is that QBs who can do both much prefer being six yards back with more time to make a decision so the pool is pretty small. Regardless we have been fallow there until Thomas, but then last year happened. (This is not to reopen the tired "different offense" argument. Just an observation.)
Personally, I think we need something that makes us "unique" so that we have a chance to compete against teams that have the supposed "better" athletes and deeper benches, and if our style of Offense, with Paul Johnson calling the plays, gives us the "edge" opposing defenses and defensive coordinators have to worry about, then I think that speaks volumes about whether we have the right Head Coach or not, and, personally, I think we do.
No doubt we have had issues with our defense, and I can't say it's because we can't recruit the "right guys" because of our academic issues, or because our players go against our running option offense more than other styles so they just aren't as instinctively reacting in "normal" offense's other teams run (I assume that's one of the arguments opposing recruiters use against us). Bottom line is that we've had really good players on defense playing under Paul Johnson, but they typically haven't played together or we just haven't had good "units" (other than the last part of 2014).