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So why is D&D 3e so complex? Do most of your sessions consist of rules lawyering, page flipping, and game speak? What can we do about it?
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When I started mastering, none of my players knew the 3rd edition, and two of them had never played a RPG at all. Being afraid they would have not come back the second evening, I started playing with only a subset of rules.
It's hardly believable how we could have played without many and many combat options (no charge, grapple, trip, disarm...), without delay/ready/refocus and without AoO, but it really helped the new players.
Having introduced the core rules gradually, we kept quite a small amount of debate/questioning per session, but we are still discussing usually, and we'll always be. Fortunately we see it as another fun of the game

You can try to delay discussion to the end of the session if it slows the game, and simply adopt (at least for the moment) a lighter approach to rules: for example, some of my players read rules by the single word as in a trial, but remember that D&D is meant to be played by normal people (and children), and sometimes things are simpler than they seem.
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Are there to many feats? To many Prestige classes?
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In my opinion there are too many PrC, but not really Feats. In any case, it should not be a problem, since each player needs to know only his own ones (few). And if he DOES know them well, the DM doesn't even really need to know them also. Players should not pretend the DM to know their PCs better then themselves.
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Are AoOs drivng anyone else crazy?
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Few (questionable) advices:
- start applying AoO only to ranged attacks and spells
- when you introduce AoO for moving, have an off-campaign session (no PC death & XP) of AoO exercise only
- keep the PHB open at the list of miscellaneous actions that provoke AoO until you don't need it anymore (a must-have table on any DM screen)
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Do any of you feel obliged to follow every rule and apply every modifier out of fear of breaking something?
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I do follow every rule without variants for now, only because I believe they deserve a chance before questioning them. And after all, I have never questioned the Chess rules because Queen was unbalanced, or Knight movements too difficult to play.

If you feel overwhelmed by rules amount, it's no crime to introduce them gradually as we did. I had never read the Grapple rules until a PC asked if he could grapple an opponent! Of course, start with basic situations, don't go too quickly to underwater battles, mounted fights, heavy weathers... most of the rules are about situations that only DM decides when to happen.