Those aren't mind control, they're mechanisms for adjudicating NPC and monster reactions.
They're mechanisms for allowing one character to control another character's behavior. Which is mind control.
In any game I've played in, a player can decide when to roll the dice. Here is one example: the GM describes the room that the PC is walking into, including the fact that within it are two orcs. The player of that PC then says "OK, I cut them down, starting with the one nearest to me!" That player has decided to roll the dice - in the case of D&D, a d20 attack roll.
That's a dodge. The player may announce an action and physically roll a d20, but it's still up to the DM to decide in game terms whether the attack happens or not and whether the die is rolled as part of it. It's much like a batter requesting a timeout in baseball-it's a request that's usually granted but it is still the umpire's decision and he occasionally rejects it.
And there are a variety of cases where the DM might decide that some intervening action or condition prevents the player from doing what he announced or otherwise rule that the action does not happen. For example, the player might have been unknowingly enchanted in a way that prevents him from making the attack. Or the rest of the party might have wiped out most of the enemies and the DM may simply abrogate the attack roll and say "never mind, assume you just mop the last enemy up". If circumstances make the attack unwise (such as a character attacking a civilian in the middle of town, or attacking a clearly superior NPC), the DM may halt the action and remind the player of the circumstances that the character knows but which the player may have forgotten or underestimated, and in rare cases may even dictate that the action does not happen (such as in a case where a player attempts to commit an evil act and the DM refuses to allow it as a form of censorship). On a more basic level, if the room is loud and the DM doesn't hear the player's request and moves on, it's possible the attack doesn't happen at all. I suspect most of us skip a player's turn now and then.
Not common events individually, but even if they don't happen, it's still the DM's choice to
let the player's attack happen, and he can still apply any modifiers he wants (and is explicitly encouraged in the rules to do so) and adjudicate the result in a variety of ways. The player has no meaningful control over any part of the action other than his character's decision to attempt or intend to perform it. That decision is important, and is the impetus for whatever rulings the DM makes. But ultimately, the player has very little control over the situation, and no D&D player ever has the right to dictate that any action happens or that any die to resolve it is rolled.
This whole thread, together with the dozens of others like it, is proof that there is no "neutral" rule set of the sort you describe. In particular, player protagonism that is a function of the GM, rather than the rules, is not really protagonism at all - as I know from my own experience, it is vulnerable at myriad points as the GM comes under intolerable conflicts of interest due to the conflicting demands of maintaining antagonism and adjudicating fairly.
I don't recall describing a neutral set of rules. The rules aren't neutral, they're simply a minority influence on the outcomes of interest, while the DM is the main influence. Some DMs are more or less passive than others, but it's still their choice to be that way.
I think that last sentence is very telling, though. The people in your experience may not have tolerated those conflicts, but that doesn't mean that they can't be tolerated and dealt with at all. Being a DM is inherently a massive conflict of interest: you're supposed to play all the NPCs, which means honestly depicting behavior that may be contrary to or antagonistic to the PCs', but you're also trying to create a rewarding play experience for the players. Everyone playing D&D deals with variations of that conflict.
And yes, players can express protagonism even when the DM controls everything. Just because he's in control doesn't mean he can't listen to the players, it simply means he has the choice of whether or not to listen to them. This is where D&D becomes analogous to the actor/director relationship in drama. An actor has to read the lines on the script, and do whatever the director says, but that doesn't mean he is exerting no influence over the final performance.
By insisting that the rules of 3E/PF not change, you are restricting all players to one approach - namely, one in which GM force is required to balance casters and fighters. That's a fine approach as far as it goes, but for those who want to play a different sort of game 3E/PF won't deliver. As I've said, achieving protagonism via GM force, while not quite contradictory, is an extremely unstable base for satisfying play.
I'm not insisting that they don't change, merely that they don't change in one particular way that I think is exclusionary and poorly thought out. There are many changes I would make. But if by restricting all players to one approach, you mean an approach where the DM is in control of the game, then yes. That's fundamental to the game.
If you want a game that posits different roles, you really should design a different game from page 1, and I don't imagine it would look much like D&D. Might it be a good game? Sure. But it's not relevant here.
4e, at least, has rules - guidelines, if you like - for the GM. It says, "Within these parameters the game will deliver what it promises. Step outside them, and we - the designers - don't vouch for the play experience you will get". This is not an issue of GM skill, then, except the skill of reading English and then doing what it says.
I think those types of guidelines are strongly implicit (and often explicit) in most games. Of course, in 3e, a lot of the DMG was devoted to talking about making various rulings and alterations and discussing the implications of them, and the first thing in the PHB is rule 0, and it's pretty strongly implied that the DM is responsible for using the rules to create the experience he wants.
