Droogie, have you and your group been playing 3E long? More than a few months? The reason I ask is that Rules confusion seems for some reason a frequent occurrance among groups that are used to 1E or 2E and start playing 3E.
The best thing I can say is that in my experience, our group, while still needing to look up rules from time to time, have become rather comfortable with 3E, and because of the conformity of the rules, rarely have to look up something (maybe wizard and sorcerer spell progression tables). Heck, the system is so regimented that I can calculate bonus spells from high ability scores in my head out to the hundreds!
Attacks of Opportunity, while important, are maybe the most confusing rules in the book. The first part is easy - within, or out of - but the rest you learn after figuring out what in combat is "stupid", and what is not. Drawing a weapon is not "stupid" - drinking a potion is; advancing on an enemy is not "stupid" - initiating a grapple with an armed fighter is.

There is a system to AoO's - one has to study it before it come out. Not having AoO's IMHO is worse than having them - In Star Wars, there is no way I cannot fire a gun at a man standing 5 feet away. However, giving him a chance to wrestle the gun out of my hand is reasonable.
The core mechanic is simple - the complexity comes in when trying to give rules for every possible action, which 3E almost succeeds at - This is its blessing, and its curse.
But I still get a smile when a player comes up with an oddball tactic, wondering how I would resolve it, and then I pick up the rulebook and tell him what chapter it's covered under.
P.S. - It's also perfectly fine to be burned out. Our group has played everything from Magic the Gathering, to Battletech, to Heroquest, to Mage Knight, to d20 Star Wars, in an effort to keep things new and spry. So far, we have been playing d20 systems weekly non-stop since January, and it may be time for us to switch systems for a while. No system will suit a group forever. It never did in the old days, and it certainly won't now.
I wonder if Piratecat's group ever gets tired of 3E? Seems as if they play it on a weekly basis too, between his and Sagiro's campaigns...