Here are the factors that influence QB accuracy:
1) their accuracy rating (duh)
2) experience and fatigue
3) if the QB is moving, their scramble skill (the faster they are moving, the more their scramble skill comes into play)
4) the distance the ball is being thrown - further distances have less accuracy. This is the only tweak I made recently, previously there was no distance penalty for passes shorter than 15 yards, I changed that because too many bad QB's were playing like superstars with the short passing game. It's possible this still needs to be tweaked.
5) Pressure from the defensive line
So you can't completely evaluate everything by the accuracy rating, if your QB is under a lot of pressure or is throwing longer passes it's going to show up in his accuracy. I'd be interested to see if you evaluate the performance with those additional factors in mind and still think the scales seemed tilted too much.
As for the defensive backs, their man-to-man coverage simply means how close they are able to stay with the WRs. But they must also have the speed to do it as well, if the WR is outrunning them then they won't be in a position to knock the ball down. That's a measure of their speed, acceleration, and weight.
Penalties haven't changed at all, if you're seeing an uptick in them the factors in that are primarily discipline with a lesser influence by fatigue and experience.