Many, many thoughts
Well, this has been an interesting read. That first post certainly does a lot to point out some of the deficiences of d20 Modern, even if you DO subscribe to the "highly cinematic is good" camp (which I don't).
I would post my two cents, but it would be more like $100. I have spent SO much time on modifying d20 for two different d20 Modern projects (Mutant Chronicles d20 and X-com d20, which will hopefully be played in the near future) that I could write for hours on this subject. I will spare you that, however, and just say a "few words" instead.
Here goes...
1) Armor
Armor as Defense works great in D&D. That's about the end of it. There are some issues there too, such as crossbows vs. chainmail, but I can get over it. Any game with magical fire swords can do what it wants as far as I'm concerned.
In d20 Modern (or any modernish, sci-fi game) things are different (at least to my somewhat discriminating eye). Armor is perhaps BEST (subjectively, of course) modeled as a combination of Defense and DR, but that can be time consuming to convert (though Unearthed Arcana has a good starting point). There are so many issues and an equally immense number of ways of repairing these so-called defects. For example, suppose you want a system whereby .50 BMG rounds totally ignore pretty much all personal armor. Simple, you can keep armor as Defense OR as DR and give all weapons a "Penetration" value. If the "Penetration" value is greater than the Defense bonus or DR, then the armor has no effect vs. that particular weapon. If you want it to be less "all-or-nothing" give weapons their own Armor Piercing value that simply subtracts from the Defense bonus or DR of the armor. I've done both of these things in writing up theoretical rules.
For X-com d20, here's what I'm doing: armor grants both DR and a Defense bonus. The Defense Bonus will be small, but it will represent the ability of armor to completely deflect some hits that would otherwise be grazes. Think of it as "Passive Defense" (from GURPS). The DR will be the main protection of the armor, and may end up going pretty high for the famous Flying Suit (a highly advanced form of personal armor...that flies). Weapons may or may not have a Penetration value. I haven't decided quite yet. The benefit of using a Penetration value is that you can keep the actual damage dice to a minimum (because instead of relying on a large die roll to penetrate DR, you simply apply the DR only if the Penetration isn't good enough to ignore it...again, you can do this partially or as an all-or-nothing gambit). Anyway, on to HP.
2) Hit Point Systems
This is also tricky in a Modern setting. In D&D, damage is easily abstracted. Whose to say precisely how well that sword hit the orc? In d20 Modern, bullets tend to be less random. That's partially covered by d20 Modern's "2dX" damage value for all guns. Two dice will tend to produce a more predictable result than the typical 1dX of melee weapons. No problems there. The problems arise with the ever-increasing hit points of characters.
There are many options. To name a few:
1) Vitality/Wound from Spycraft or Star Wars.
2) Stamina/Lifeblood from T20.
3) Damage saves from Mutants and Masterminds.
4) Massive Damage from d20 Modern or CoC.
5) Simple HP from D&D.
What works best is going to depend on the feel you want for your campaign. (Duh). Personally, I think the T20 system doesn't work too well, especially when you take into account the weird armor and the relatively unfinished nature of the rulebook. There is a concept that I have borrowed from Dream Pod 9's Silhouette game system that will hopefully work very well for me. It's very obvious, and likely many people have House ruled it into their games already in one form or another.
Thus, X-com d20 will use a sort of scaling threshold massive damage system. The idea is simple. Using the basic concept of the massive damage save, I will create a number of thresholds whereby the effects of even TAKING that much damage start to have serious consequences. Likely, it will look something like this when I'm done:
1/2 Massive Damage Threshold (as figured using normal game rules): Flesh Wound. Make a DC 10 Fort save. Failure indicates that you have been Stunned for 1 round. Success indicates that you are merely Dazed until your next turn. A -1 Wound penalty applies to all future skill checks, saving throws, attacks, and whatever else you think it should apply to.
MDT: Deep Wound DC 15 Fort Save. Failure indicates that you are instantly reduced to -1 HP and are dying. Success indicates that you are Stunned for 1 round. Furthermore, you are Fatigued regardless of the outcome of the save. (This limits movement, I believe, but if it doesn't, it should.)
2x MDT: Mortal Wound DC 20 Fort save. Failure indicates that you are instantly reduced to -5 HP and are dying. Success indicates that you are Stunned for 1d4 rounds. Furthermore, you now take a -3 Wound penalty to all rolls. Additionally, you are considered to be Exhausted until this Wound is healed.
And so and so forth. At the GM's discretion, you can include simple bleeding rules (I recommend 1 HP/minute for Flesh wounds, 1 HP/round for Deep, and 1d4 HP/round for Mortal wounds). I have rules for multiple wounds and how they can be treated with First Aid and the like.
Once I develop them more fully, I may go ahead and post them if there's any interest (there really wasn't at the official d20 Modern forums, but if it's different here, I'm happy to share.)
There you go...that was a lot more than 2 cents, but hopefully not too bad.
-Apoc