So, on their own, all these rules make a lot of sense for me.
Concealment is just making yourself more difficult to see - if you can't properly make out the outline of your enemy, if you can't find identifying features to give you an idea where the rest of its body is, you're going to have to get a little lucky to hit.
Soft cover doesn't include a reflex bonus because the guy in front of you is not standing still taking that fireball or that grenade.
Cover seems fairly simple - measure the angle the attacker's hitting from, assume character occupies a quantum state in his five-foot square (since at any given second he could be peeking around the corner he's got cover from, ducking into it, etc.), then estimate a reasonable percentage of the victim your attacker can see, choose the appropriate cover modifier. You're unlikely to find improved cover without a prepared battlefield, but a smart character can do a decent job of ducking from obstacle to obstacle to get to the front line while looking somewhat invincible. Of course, cover depends on your GM's creativity, so some games see a lot of wide open spaces with no obstacles for climb checks, no cover, etc.
Prone and kneeling are simple and easy to picture. You make yourself a smaller target relative to your attacker.
But isn't that what cover does?
There's a fundamental assumption with cover - the attacks you're taking can't just pierce through it. If you're hiding behind a wooden counter and a fireball on the other side does enough damage to destroy the counter, you're probably going to get burned and take splinters. You're in a better position than if you were standing in the open, but if that countertop were made of, say, stone, you'd have total cover and not even have to worry about the fireball.
Now, this gets sticky when you run, say, a Guns Everywhere campaign. As soon as a gunslinger has a working rifle and a decent DEX bonus to damage (and with Guns Everywhere, that starts are first level), start looking at the Damaging Objects numbers for wood - the thing to consider is that wood has DR 5 and not a whole lot of HP. Many great movies with well-done combat scenes have entirely realistic moments where one side just decides to spray through the other side's "cover" and take them down through the sheer mathematics of covering an entire area with bullets. It might take time, but it makes sense, and while the rules may not directly address it, they imply it - concealment is the appropriate defensive bonus in this situation, as concealment is just when you're harder or impossible to see, but don't have actual projectile-stopping assistance. Personally, I half the ranged damage as normal against objects, apply the object's DR, and then deal the remaining damage twice - once to the object, and once to the defender behind it (if the attacker makes his concealment roll, of course) - while keeping a rough idea how much HP is appropriate for the object he's hiding behind. Once it's broken, I reduce the concealment check either from Total Concealment to Concealment, or from Concealment to Partial Cover or no cover as appropriate. It's a bit more management, but I think it's a fairly logical and highly cinematic way to handle these sorts of things. Sometimes I like to force knowledge checks for the materials people hide behind - if they fail, they're flat-footed the first time someone tries to shoot through their cover.
But then there are interesting situations that crop up. Assume someone's behind a thick stone wall, taking gunfire. For the purposes of this thought experiment, assuming the wall is impervious to gunfire. It's a low wall, but the defender is pushed right up against it, kneeling down, and the attacker is farther from the wall on the opposite side. What is the defender's AC bonus?
+4 from cover, +2 from kneeling? But does this make sense? Cover and prone/kneeling bonuses both seem to work on the idea that you're presenting less of yourself to be attacked. If an attacker high up in the air shoots down at buddy at the rock wall, it seems logical that he wouldn't be dealing with the cover bonus, or it would at least be lessened given that from his perspective, it's not as good cover as it would be against the dude opposite the wall. Which begs the question, if you're in the air directly over a standing, oblivious target, does he get the +4 prone bonus? Technically, you're attacking from the angle that makes him the smallest target.
And let's take a gander at the idea of using dead bodies for cover - gruesome as it is, in a world where you're fighting assassins, orcs, and dragons on a regular basis, you're going to reach a point where you have to do something gross to survive. Standing and even kneeling with a dead body only makes sense cover-wise if it's an oversized creature. But with two medium creatures fighting eachother, using the dead bodies of medium creatures as gunfire cover, what do they get? +4 for cover, another +4 for prone? This seems a little excessive, but it _does_ seem to make a certain amount of sense if the angle of attack is right: if the other guys is prone on terrain level with you, well, you're really not showing him much of yourself to hit. I've toyed with the idea of just upgrading the cover based on positioning and angle of attack and it makes sense when you're going prone behind a low wall and thus upgrading to total cover, but that starts to prove troublesome when feats like Improved Precise Shot come into play - if he's instead kneeling behind that stone wall, and IPS ignores cover, he should probably still get a +2 from kneeling.
So is kneeling and/or falling prone a requirement to take advantage of some kinds of cover? Should the bonuses stack? Or should I re-examine and make a special ruling for each situation as it crops up? Any thoughts on my handling of low-DR cover? Does soft cover stack with cover? I've been thinking on these ones for some time, and have found the proper visualization of the rules difficult for this one. I could use some advice.
