Agility doesn't directly affect pass quality. The 2 things that Agility does are
#1 reduce the amount of time between when a QB decides to throw and actually throwing (release time).
http://glb.warriorgeneral.com/game/replay.pl?game_id=2932263&pbp_id=538464 you can see it pretty easily on rookie dots. The QB has the target, and before he throws, you can see him "wind up" when the football on his dot moves backward before the launch.
If there's a defender closing in, and the QB doesn't have a lot invested in Pocket Presence, then his pass quality will go down from pressure. The trick is.... Quick Release also affects this and overrides whatever Agility is when it fires (75% of the time). Pocket Presence reduces the effect the increase in pressure, actually has on the throw.
#2 Agility is also the amount of wiggle your QB has while in passing mode. High Agility will give him more opportunities to move around. More speed will increase the amount of space he covers per move. Think of Speed as miles per hour or more like inches per fraction of a second.
The bottom line is you can make a better QB by taking the SPs you'd invest in Agility and Speed (say going from 1-cap to 6-cap each--maybe 70 SPs) and using those SPs on more Strength, Vision and/or Throwing. I've given up on Confidence theory, for QBs.