I don't see this as just being about simulationism. It's about not really taking into account the contributions of the players to the plot in other than superficial ways ("do you want to win the battle using your axe, or using your sword?").
Wow. This sounds rather bitter and petty. Different games allow different amounts of player contribution to the plot. The default assumption in 4e is that the DM comes up with the plot, the players play through it, but at certain points along the way, they'll come to "Decision Points" which let them affect the outcome of the plot.
For instance, the DM decides in advance that the forces of the Evil Archmage will attack the town the PCs arrive in. After the battle the PCs will be approached by the Mayor who asks them to figure out who is behind the attack and to stop them. At this point the PCs decide which way they will go, how they will figure out who the attackers were and so on. Their skills will affect how fast they find the information, what information exactly they do find, and so on.
That's the default assumption. Some people don't like that and allow PCs way more control over their plots. That's fine.
If you are talking about games where the PCs get to walk into a town, kick the drunk off his chair and decide to make him run for office and become the puppet mayor for them not knowing that the town is already ruled by an illithid with a disguise spell up....yeah, that's a completely different sort of game than the default assumption of 4e.
4e assumes more of an interactive novel than a blank 3d space filled with programmed objects waiting for the players to run around in. Some of the goals of the plot oriented, DM controlled game are not compatible with giving your players the power to go wherever they want and do whatever they want.
If you know the mechanics of Orcus' gate spell, for example, you can fairly judge the player's various attempts to close it (or respond to the uses of the Arcana skill) and define it's limitations rather than just arbitrarily decide based on some plot agenda. Combat and Skill Challenges are handled this way already. Why do monsters even have stat blocks? Why doesn't the DM just decide when they die rather than having to track hitpoints and 5-foot steps? The DM following certain rules behind the scenes isn't alien to DnD. In fact, it seems to me to be a central part of 4E. Still.
Because there are 2 parts to a game: Story and Game. The game portion is interactive. Your players roll dice to determine the outcome. The story part is not.
Also, why is a plot agenda unfair? I find a game much more fun as a player when it goes like this:
Portal appears in the middle of town, undead swarm the town, the PCs save some people but are forced to flee by the overwhelming number. They decide to go to the capital where they search for any information on what this portal might be and how to close it. They find a cleric at a temple who identifies it as a portal to the realm of Orcus. He knows of a Ritual to close it, but it requires 3 rare spell components to complete. They go on a series of adventures to track down the items. During their adventures, they are attacked by minions of a powerful priest of Orcus who wants to stop them, they eventually find all the components and proceed to the portal. There, they meet the priest of Orcus who has gathered to stop them personally. They defeat him. They do the ritual, only it doesn't close the portal. They hear laughing from inside the portal and Orcus himself comes to crush them. They defeat him, and with his last breath, he is sucked into the portal which closes behind him. The world is safe.
Rather than:
A portal appears in the middle of town, undead start coming out and a PC announces, "I use Close Portal, it is a spell from the book. It closes any portal. This is a portal, it should work." And the DM says, "It doesn't work on this portal." The player says, "What? Aren't we playing by the same rules here? You are going to tell me the rules don't apply to this portal? That's stupid." The DM says, "Fine. It closes the portal. The world is safe. The game is over."
One is a result of following the rules whether the plot works or not.
The whole point of Skill Challenges was to provide a more mechanics-based system for resolving events. Saying "it's not used in combat, so I can just make up the results based on plot considerations" could be used for PCs Diplomacy with the King as well. But really, if you're a story teller and you want to follow plot considerations instead of following rules then why are you getting involved in rules discussions anyway? Who cares what the rules decide to cover - just ignore them as you do anyway.
Because a game with no choice and no randomness would be no fun at all for the players. You want them to have fun. Most of the random chance in games is heavily slanted in favor of making things come out the way you want it to anyways. The combat rules give the overwhelming advantage to the PCs, so they'll win almost every time. The new skill challenge rules mean the PCs win a skill challenge the vast majority of the time.
I decide what NPCs due based on the whims of the plot all the time. Nothing in the Diplomacy skill ever says "By rolling high, an NPC will agree to whatever you want. By rolling low, he'll immediately disagree." I often decide that "despite your poor roll the King agrees" or "despite your good roll, he isn't convinced".
I, as a DM, treat the game as 2 different games with 2 different sets of rules. When it is combat or skill challenge time, whatever happens happens. Follow the rules exactly as written. It'll be a fair decider of whether you succeed or fail at your task. When it is plot time, I will accept input from the players and try to take their actions into account, but I will not allow their decisions to simply override everything I want to happen. They certainly might get bonuses and benefits. I might decide to modify things if they give me an idea that is better than what I originally thought of. But, if I've decided that the only way to close the portal is to kill Orcus at the end of the adventure, nothing they do is going to change that.
However, if your players are under the impression that you should be following the rules, and that's the reason that additional rules cause you heartburn (because they'll call you on them), then I think you have bigger problems. The solution IMO would begin by being honest with your players about what kind of game you want to run and outline which types of rules, if any, you intend to follow.
Why is this a problem? I expect everyone playing any game to follow the rules. That's the point of playing a game. I certainly expect my DM to follow the rules. I expect the DM to make up fair and fun rules when there aren't some available. I think rules directly related to combat should be adhered to. That's when it is the most "game-like" to me. In the same way that I'd want everyone in a monopoly game to play by the same rules, I'd probably bring it up if a DM just randomly broke them. But, I give leeway for there to be sections of the game outside of the rules. I don't have a problem with a monster having a power I can't get. That's part of the rules. I don't have a problem with there being exceptions to rules. Like a specific portal that has different properties than most portals and so on.