Sounds like an interesting project in the works, always good to see actual numbers being crunched. Also appreciate Ziegander approaching this divisive topic so civilly.
Here's my issue: The CR system sucks. It fails to account for differences in power and versatility between class/feat/spell choices, which is kind of the point of this discussion. But it also ignores differences in tactical ability, system mastery and party composition, not to mention the rock-paper-scissors way in which monster and character abilities can interact. It is not hard for a competent GM to crush even a decently optimized and played party with a CR-appropriate encounter, should he decide to do so, simply by metagaming and playing to the party's weaknesses. I don't hear anyone advocating this kind of adversarial GMing, but as GM fiat plays such a heavy role in determining encounter difficulty (it is equally easy to throw a CR-appropriate softball encounter to Team Gimp) I find it hard to accept the CR system as a basis for objective character standards.
There must be some objective standard, as otherwise the game is Magical Tea Party and not Dungeons & Dragons, but I would set it at an extremely low level. I'd put the 'armless archers' and unoptimized Truenamers of the world below the acceptable threshold because their abilities just don't function. However, I'd let an unoptimized Bard 4/Cleric 4 onboard the ride because even in a theoretical houserule-free game I believe there is a reasonable expectation that the GM will base encounters around the actual abilities of the players. This can require deviating from CR guidelines if PCs are exceptionally strong or weak for their level, but that doesn't necessarily make it a houserule:
Dungeon Master's Guide 3.5, pg 48
"A tailored encounter is one in which you take into consideration that the wizard PC has a wand of invisibility and the fighter’s AC is 23. In a tailored encounter, you design things to fit the PCs and the players...
A status quo encounter forces the PCs to adapt to the encounter rather than the other way around. Bugbears live on Clover Hill, and if the PCs go there, they encounter bugbears, whether bugbears are an appropriate encounter for them or not. This kind of encounter gives the world a certain verisimilitude, and so it’s good to mix a few in with the other sorts of encounters.
If you decide to use only status quo encounters, you should probably let your players know about this." (emphasis mine)
While a difference in GM worldbuilding style shouln't really be called a houserule, the last line leads me to believe that tailored encounters (with a smattering of status-quo ones thrown in) should be considered the default expectation in D&D. I just don't see how any objective standard beyond basic functionality can apply in such a case.
