I wasn't really comparing it to '06. I was just pointing out the gameflaws as I remember them. On the QB completion percentage, I actually played several games where QBs would have ridiculous days, completing 22-23, or something like that. But you're right, it was probably closer to reality than what we currently have, because it rewarded you for being patient and hitting the guys underneath, rather than just throwing streaks all game.
The only thing about 2006 that I really like over 2004 is that you have a better ability to adapt your strategy to what your opponent is doing. Things like coverage audibles, or hot routing guys to blitz or spy, as well as having the 4-2-5 and 3-3-5 defenses just make it better from an online perspective. Vs the computer they might not really matter as much, but in a head to head game, it's nice to be able to customize your defense to try and stop whatever your opponent is doing. And offensively, you have more options with motioning, packages, and the ability to change the direction of a run at the LOS, which keeps the defense from just loading up on the strongside, and leaving absolutely nobody weakside.
I think that the zone coverage on NCAA 2006 is fairly realistic. The only thing that I'd agree with you on is the fact that LBs are too athletic in being able to deflect balls. As far as having 5 defenders converge on the ball when it's caught, I'm actually having opposite problems, with nobody taking an intelligent angle or reacting quickly, regardless of AWR.
I will say this about 2004. For being 2 years ahead of 2006, it was WAY better for it's time. If you kept the 2004 gameplay, made some minor adjustments to zone coverages, and added in those little things that I talked about earlier (coverage audibles, flip the play at the line, package subs, etc...) then I think you'd have a MUCH better game than what we got with 2006 (or 2005). The core gameplay just seemed to be a lot smoother and more balanced.