This has been a really interesting thread. I always know that is the case when I am nodding my head and saying "good point" to both sides of an argument. (Yes, I nod my head and talk to my computer screen. Don't you?)
My take up to this point is this:
I agree that it makes little sense not to allow AoO's on helpless foes. There is however, IMO, no chance that the 3.5 rules will address this.
If I were going to allow AoO's against helpless foes, I think that I would feel forced to do a few things for the sake of balance:
1) Restrict the number of AoO's against a given helpless foe to one per attacker. I'd use the fairly flimsy excuse that being helpless is a single circumstance and you therefore don't get multiple AoO's deriving from the same circumstance.
OR
2) Add additional prerequisites to Combat Reflexes to assure that it couldn't be taken until higher levels.
AND
3) Ease up on the "Death Rules" such that combatants didn't die until they had taken more than -10 HP. Negative Constitution score seems ok early on, but that will be negligible protection at levels 5 and higher where any given attack against a foe rendered helpless by unconciousness will be tantamount to a CdG (which is NOT an evil act by the way

).
To be perfectly honest, I probably won't do any of that and will just ignore the problem. I understand that for some people, this will be the pet peeve that they MUST address with the system. I respect that but this one isn't mine.