If the GM pulls out "special measures" - like the king's own diviners to protect the chamberlain from Charm spells, or the replacement lizardman guard to get in the way of Magic Jar - then from the players' point of view, in my style of play, this is a type of ad hoc punishment for good play (@Manbearcat's Calvinball). If the player holds back him-/herself, then s/he is no longer going all out to bring his/her PC into contact with the fiction. S/he's voluntarily forfeiting the ability to deploy resources. For me, at least, this is insipid, and turns the player into a type of co-GM and the character into some sort of half-way thing between PC and NPC. That has little attraction for me.
I still think you are misframing the argument and mischaracterizing those who do not see wizards as a problem. Charm Person is a perfectly fine spell, nothing wrong with it, and it should work as written. I have no balance worries about it.
There is a conflation of two different arguments here: playstyle and mechanics. While the arguments feed into each other, they are separate arguments. In part, the playstyle of some of us helps keep the casters in line by enforcing in-game consequences for failed actions. If the wizard is caught charming the chamberlain there should also be consequences. This is not punishing the player. Nor are these special measures meant to make the spell "not work." It is simply having the game world work in the way the GM thinks it should work. This is a play style issue granted, but once that is granted, why villify the players and GMs who like that sort of play-style. Its not holding back wizards and more than having the castle guards show up to arrest the fighter for murdering the innkeeper is "holding back" the fighter. But all of this is playstyle related, it has nothing to do with whether the spell would work or not as written
I contend that most of the spells as written, invisibility, charm, magic jar, are not, imo, game-breaking. They work just fine and create some interesting solutions to problems. They do not, of themselves, unbalance game play, nor do they make other classes obsolete. Groups in which this happen, have, imo, a different problem than the mechanics, or they are failing, in some way, to fully apply the mechanics. This does not mean there cannot be improvements to the spells (cf. Polymorph and Pathfinder), but on the whole they work pretty well. I have no problem, in my game, with wizards pushing hard to fulfill their characters. Let them do so. The game will function and be fun if I do my job right as a GM.
Now, if the mechanics do not work up to specs for your preferred play-style, I sympathize with you, but this proves nothing about the viability of the mechanics themselves to function as needed for the game they were designed for. I am not sure what your goal is at this point. You acknowledge 3.5 and PF does not seem to work for you and you do not like the basic playstyle the game was meant for. I am sorry for that. But it works for the rest of us, so why keep insisting that we agree the game is broken or that the spells don't work? Find the game that works best for you, or design it. Explore your game-theory to your heart's content, but stop trying to insist that others agree that your view of the spells must be the correct view.
And may I just add that to keep accusing others of playing "Calvinball," simply because you would do it differently, is rather meanspirited on your part, slightly slanderous, its getting old, and its especially grating because it fails to acknowledge that nobody is actually arguing the DM should just change the rules to suit his own tyrannical whimsy or preset story-line.
