Please note that while this is a criticism on the d20 system in its ability to emulate actual situations, this post is not a criticism on the balance of the game, I think it's runs alright as is, and I'm not really a fan of rules bloat.
Let us take charging. You move your full movement and make a single attack at your BAB +2. Let's say that this target is an apple on someone's head, the d20 rules have it so that it is easier to hit it while running at it than to just stand there and hit it... Hopefully most people will realize that it's actually harder to hit something while running than to hit it while standing still. Giving the charge action more thought, some may realize that the bonus comes from catching the target off guard. In most situations, catching someone off guard makes up for having less accuracy when running.
Obviously inanimate objects are always off guard because they don't have the ability to be on guard, making running at it seem unintuitive; however in the d20 system it's easier to hit if you run because it doesn't make that discretion. In fact even those who can't be caught flat footed can still be charged. Perhaps charging is using more power from running, but in that case why doesn't it also do more damage and why does it work with finesse type attacks? Either way, charging to better hit an apple on someone's head still doesn't make sense while being rules legal.
However you can't just say that charging makes a character flat footed, because that would be too powerful and would unbalance the game; even if you added in a to-hit penalty. While being charging might catch someone a little off guard, the target can still react to it.
In the game there's no such thing as half flat-footed nor just an off guard condition/bonus/penalty, and the only penalty for moving is that you can only make one attack (which doesn't really matter until 6th level and beyond) instead of just a penalty to hit. Also, since the weapon you wield doesn't change how well you can handle it (I've never witnessed any game system that makes heavier/larger weapons harder to wield when moving, rather at most they just hinder movement itself but hit just as accurately), in game it makes more sense to pick up the largest weapon you're proficient with when you go to charge or spring attack. It's just more efficient to spring attack with an great axe than a dagger in a game. If there is a game system that does decide to implement to-hit penalties from movement, I would hope they lessen or not apply those penalties to light weapons.
Just some food for thought.
AC is also a measure of the hardness of your armour. When you charge, it is easier to break through armour.
Hitting something doesnt just mean making contact with it. It means injuring it. 'To Hit' in not exclusively a function of accuracy. It is also the power behind a swing/attack to punch through armor/thick hides. Charging at something/someone helps you punch through armor, which adds to AC, so it gives you an attack bonus.