Great ideas abound here!
Some thoughts on realism:
I think the general problem can be summed up by saying that, in real life, a great many things are HARD. In a realistic game, these same things would be hard.
1) Hitting your target with a gun is not an easy operation. A scientist who starts out swinging at things with a crowbar (Yeah, HL is cool.) shouldn't even be very good with that -- at least at first (more on that in a bit). But an M9 pistol? Better be D&@N CLOSE! Shotgun? Well, sure, he can make hits, but wild misses just as easily if he's not concentrating and taking his time. Two points here: One is that an aimed shot takes time. I don't think that the player should have to align the sights manually, but he/she should have to give the character time to get as set as he is able in order to make the best shot he can. Maybe a second for an aimed pistol shot, and a couple of seconds to steady a rifle. And a shot while moving is something like 5 times harder. But here's the rub (and point two): his best is none too good, at first, but I think he should improve. Perhaps in the old manner of character or experience points from the old RPGs, a character's skill with a weapon should improve with the number of shots taken -- gaining relative skill quickly at first and then more slowly as he/she advances to more mastery, and maybe even with the number of AIMED shots taken (rather than spray and pray). It would be quite an incentive to keep a weapon your character has used a lot. His/her abilities could increase in general, but much more significantly with that weapon. I might shoot a 1911 fairly quickly and fairly well. That doesn't mean I can hit my own car from the inside with an RPG-7. And what about the bad guys? They're trained (to one degree or another) soldiers/combatants, too. Why should they not be as good or even better than you are at this? That is a real issue. One generally develops a sense of super-humanity in a lot of these games. Play should realistically balance your cunning, stealth, and *maybe* like *one* special skill against realistic mitigating factors (complacency, tiredness, distraction, etc.) that your enemies might possess.
2) We've covered the problem of carrying 15 large weapons and several 1000 rds. of ammo. But, truth be told, most of the games I've seen provide so very much ammo just lying around that they lack any kind of credibility. I mean, even on a military base, you aren't going to find crates of ammo, grenades, rockets, etc. in hundreds of spots just waiting to be found. This is sometimes dealt with a bit more realistically (robbing the dead or breaking into storage areas) but it should still generally come with choices: "I'm almost out of 5.56. If I kill this "terrorist" I can take his ammo, but it's 7.62x39 or 5.45x39, so I'll have to take his rifle, too. (See section 1. What if I'm really good with my M-4? I'll lose a lot of my experience advantage if I change platforms.) If I take his rifle, will I leave my M4 behind or try to struggle along with two? What if I have to set down something important in order to do so? What if I can't run very fast with all this extra gear? Etc." It would be quite realistic to start a scenario with one weapon and maybe two mags and if that isn't enough you'll have to improvise and/or take what you need from your opponents. Not just look behind that stack of tires in the motor pool and there's 4 open ammo cans of your choice stuff.
3) We've discussed how sound is a lost concept in most games. I LOVED the idea of loud gun shots making ambient noise suppressed for a LONG time, but maybe you could find realistic gear like ear plugs that could help with that. Seems picky, but you are going to be in a distracting amount of pain after firing too many bursts from that M240 inside a concrete building without some ear protection -- and you won't hear your enemies advancing as well as you could before.
But, on another topic, gunshots are loud and very discernible to anyone trained with weapons. If I fire a .308 on a street, everyone for about 4 blocks in all directions should know about it. Fire a pistol indoors? Well, folks outside should have heard it at least, and the enemy within earshot should react immediately. (This could be modified to great effect by the loudness and type of ambient sound, too. Is it a quiet spring day in the woods or a thunderstorm at night in a foundry?) You just alerted them to your position and gave them a pretty good idea of your position. Further, it is hard to imagine a modern scenario wherein they wouldn't use their communications gear to let their whole chain of command know. Sucks, but that's the way it really is. (It's hard/frustrating, like I said.) You've alerted the neighborhood? Well, then you're going to have to vacate. If your movements are covered by a further barrage of gunfire (that doesn't kill EVERY enemy in the area), you're going to have an even harder time losing your trackers. This greatly restricts game play, but the story line could be written to work with it and it would be much more realistic.
4) Again on wounding: Yes all guns should have wounding potential roughly equivalent to their realistic capabilities. But getting wounded SUCKS! Yeah, you've got your Level III vest on and can't run all that fast, but you just got shot in the LEG by a guy with an MP5. Ok. Assuming it missed the femoral artery (and/or you got medical attention immediately) you aren't dying and probably killed off that guy, too. But, you shouldn't then be running around like nothing's wrong. A lot of people have complained about hitting someone in the foot with a .50 cal and he dies (or doesn't). Well, he sure is VERY NEARLY out of the battle for good, unless he has no choice but to fight on, but his level of effectiveness is going to be 1/2 or 1/3 of what it should be and if he does fight on, it will probably become WORSE, not better. And that works for both good guys and bad. Shoot a bad guy in the leg and he should require assistance just to move very far/fast. And guess what? You got shot in the face with a .380? Dead. That's it. Your trauma plate didn't help. Yeah, that's a very lucky shot (or a close up surprise) but that is how it works. Blown clear of a vehicle by an IED? Well, your armor didn't *just* soak up quite a shock. It may have saved your life, but your body is in a seriously compromised state and without help, you will probably not make it out alive. You probably can't hear or see. Maybe ever again. Certainly, you won't be in fighting trim.
And, if you're in a combat situation and are are still fighting after 10 or 20 hits to your armor and various minor wounds, well, that's amazing, but your days are numbered. No amount of med-packs and health-ups will put you back to 100%. And, throughout the course of the campaign, your "MAX" condition should reflect that. Sad but true.
5) Chaos SUCKS: Bullet don't penetrate when they should. Or do when they weren't expected to. As noted before, wounding hits may be very serious, even if you're wearing armor and the caliber was small. Shrapnel might kill you, wound you, miss you (blast damage is another topic) but them's the breaks. Wind gusts deflect bullets, as do foliage, obstructions, etc. Guns jam. Sometimes they break for good. Sometimes objects just don't work right or at all. Surfaces are slippery, sometimes you trip over things or become entangled. Vehicles run poorly (especially with damage -- and then, not for long). Etc., etc.
These are VERY challenging points to design a game around. But when someone figures out how, boy will they have the game world by the throat! But, as someone pointed out, there would be a lot of folks who would not feel it was "fun," so it would get a bit of bad press, too.
Whew! Come on folks, there's more like this! Help me think of more!
-Sam