I'm not sure which simulation I prefer. However, the following are issues that affect my simulationist preferences.
1) Absolutes: I generally don't like automatic immunities for races and classes except in instances where it makes sense (e.g., Constructs and undead immune to poison and disease, a creature of fire immune to fire, etc.) or spells that provide absolute effects to things that are skills (e.g., know direction, knock, jump). The latter should provide temporary bonuses to skills. Even for most trained skills, I think untrained characters should be able to attempt a skill. I think Sean Reynold's article explains fewer absolutes very well (then again, I asked for fewer absolutes in my pre-3e questionaire feedback)
2) PCs being special just because there PCs: I' m really not keen on seperate mechanics for PCs and NPCs. Take NPCs classes for instance. I don't like the adept and warrior npc classes. In my opinion, any pure caster should be a cleric, druid, sorcereror or wizard. Warriors should just be low level fighters.
The one exception is Action Points/ Fate Points, etc. I like players having some protection from bad rolls.
3) Races: Unless we are modeling a specific universe (Star Wars, Star Trek, Marvel, DC, some fantasy novel, or tv show), I prefer cultural aspects to be removed from race. Actually, even for a specific universe, I would prefer having cultures seperate from biological aspects. A human raised by Vulcans or Betazoids would be an interesting character.
4) Skills: As a player, I like skill ranks and detest the skill mechanics of Star Wars:Saga Edition. I don't like the idea of my character's skill bonuses automatically improving just because they have gained a level. I prefer determining my character's initial skills by their background and improving skills which my character had opportunity to develop either through practicle experience or training with someone.
5) Combat:
a) I prefer the mechanics of Mearl's Book of Iron Might to Tome of Battle: Bo9S. There, imo, should be a gamble to trying either fancy maneuvers or targeting specific locations with payoffs (more damage, inflicting effects, etc.) with the risks for attempting a maneuver being a deterrent from repeatedly using the most powerful maneuvers- the exception being the attacker outclasses their opponent or their opponent's defenses are down (e.g., being caught off-guard (bluff/feignt), dazed, stunned, etc.). Maybe, its having some training in martial arts and boxing, skirmishing with people much more experienced in weaponary, watching Van Damme and Seagall movies, watching MMA and san shou fights, etc.), but the idea of limiting a non-magical maneuver by something arbitrarty as per encounter just doesn't seem right. A player should be able to have their character repeatedly attempt maneuvers even when it is not wise to do so.
b) Sneak Attack, Precise Strike, Skirmish, etc. as class abilities: I don't like the idea of sneak attacks, precise strikes, skirmish, rage, etc being limited to a certain class. They are abilites that anyone should be able to learn without having to take a new class which brings along new baggage in the form of other class abilities that the character never had the opportunity to develop.
6) Magic: I don't like the idea of wizard always being able to cast something (well, maybe cantrips are alright I also prefer non- per encounter (as presented in TOB and Star Wars: SE). Per encounter has to many thing that just don't stand up to examination. The maneuver is tiring? So why can use another maneuver that's more strenuous or of equal power? Encounter as a unit of time? Why can I use a manuever in four subsequent encounters in the same time period it takes for one large encounter in which I can only use the maneuver once (not including rechaging). I'd rather not have per encounter and have the maneuvers drain some kind of energy that moves one along the condition track (which seems to model several sources of fiction).
7) Other elements:
Level draining and EXP costs to balance the casting of specific spells or magic item creation. Levels and EXP don't exist in the game. Using them to create fear or balance in game actions is not something that I like. Ideally, my preference would be for experience to simply be when you level and level to be simply a period when you improve your character develop new skills and acquire new feats and spells (if using previous editions of DND), etc.
A target's Hit Die or level directly reducing or negating a spell's effect: I don't mind saving throws, but saying a character is immune to effects because they are 10th level or are dazed instead of stunned, etc. because of level is something I don't care for. Use saving throws and have staged effects by how much the target fails the save.
8) Changing things like a rust monsters attack so that it is temporary so that players don't have to leave the dungeon, use another weapon, etc. Stuff happens. The life of an adventurer is not all sunshine and roses. The character is supposed to be a hero, so find
another solution (or has the old Mayfair DC Heroes game pointed out, Batman doesn't complain about the unfavorable situation he is in, he tells himself that he needs to get out of the situation, "Now!" and finds a way to do so).