This section ends up including one of the most radical of the changes, so I'll begin on more familiar ground: In this "d20 Rethought" system, hit points are replaced by what amounts to the Vitality/Wounds variant from d20 Star Wars/Urban Arcana, taken a step further and merging critical rules from 4th edition and Spycraft.
All characters have vitality points (dependent on Stamina) and wound points (dependent on Brawn). The latter represents their ability to withstand physical harm, while the former represents their ability to parry, roll with or otherwise negate an injury that they would normally be unable to avoid. When a character takes damage, they lose that many vitality points; when damage would reduce their vitality points below zero, they lose that many wound points instead. When your wound points go negative you're now helpless (still conscious though), 1/10 chance to stabilize each round, -10 equals death, yadda yadda you know how it goes and I'm not writing a rulebook quite yet. Here's the meat of the matter:
-This isn't going to be a system for high-powered magic; healing won't be a big factor.
-Your starting wound points equal your Brawn Score plus your character level.
-Wound points recover slowly, probably at the same rate as D&D's natural healing.
-Your vitality points come from your class, same as hit points except that you get double the max die result at 1st level and the dice range is d4, d6 or d8.
-Under normal circumstances, you start with full vitality points at the beginning of each encounter.
-Your vitality points are tied to fatigue, in that losing them wears you down (exact mechanics are still a tad uncertain, I'm not sure how similar I want fatigue to be to D&D). You can also spend vitality to invest extra effort in an action, generally through a feat or class ability.
-Certain effects can temporarily decrease (through disease and injury) your maximum vitality score. These are the sort of things that reflect a general weakened state on a character's part.
-Critical Hits: Normally crits follow 4th edition rules; there's no confirmation roll and no multiplying damage, a crit happens as soon as you roll that 20 and the result is that your damage dice are maxed. HOWEVER. d20 Rethought features action points, and without going into much detail here both GMs and players have a supply. Whenever you get that critical and the opponent has vitality points remaining, you can spend an action point to give up the maxed damage and attempt to deal damage straight to their wounds instead. GMs can also do this; so, there's always a chance for that lucky shot to head, but a dramatic limitation is in place that prevents this from happening on a regular basis.
As for the mechanics: you make a confirmation roll to hit and reroll damage. If the confirmation roll succeeds the damage goes straight to wounds (and confirmation rolls can crit as well). But if said roll fails you're dealing that rerolled damage to the target's vitality first, as if the crit never happened; there's a bit of a gamble here.