Some of that has to be a slider setting. Next, I don't know what QBs you are talking about, but D. Brees and P. Rivers are the top two deep accuracy QBs in Madden, and the only two with 90+ deep accuracy, who also only have 88 throwing power. Under 90+ throwing power isn't that big of a loss. The 87/88/89 throwing power range is still
very good. Also, check the medium accuracy of those QBs. There are a number of QBs with mid 80's medium accuracy in the default rosters. This is also a very nice stat. The real issue with a lot of QBs in the NFL is their "awareness." Sure, Manning, Brady, Rivers and other can throw the ball "on a rope" but they also understand coverages. This is the awareness rating.
In real life, it takes a lot of skill to drop back, read the defense, make the correct choice of where to throw the ball with bigg offensive and defensive linemen in your line of sight, knowing you only have around 3 second to make that choice, and then also have the arm that can get it there. QB is one of, if not, the most difficult job[s] in sports. In Madden, outside of throwing acuracy, most of the rest of these skills are lumped into a generic "awareness" rating. Also, i wish there was a computer awarenss/ball carrier vison slider. We have a run reaction and pass reaction slider for defense that directly relates to defensive awareness. We should have the same for offense. We could improve the computer running game [or should] by boosting that slider [if it was real] and could tune QB play as well.