Having Skimmed the Tread I would like to add some thoughts.
Considering the system was designed when Heavy Fortification was going to be very very rare I agree the system needs at least a number of adjustments to compensate for how common Heavy or 100% Fortification now is.
Fortification matters really to two types of characters, those that get hit a lot and those that get infrequently.
The problem with the current system is that it allows players who get hit in-between amount, neither a lot nor a little, to extremely minimize the characters risks with minimal investment. Or in simple terms it is easier to Min/Max a character because of Heavy Fortification items (cough Minos cough and I guess the new CC pirates hats too).
While I like the basic concepts present by Inkblack I worry that Casters are again going to take it in the shorts due to their low basic HP and now increased vulenrability to damage spikes. Hey I just took 350 points damage on my Sorc thanks to the Crit. To counter this I am guessing a Spell or Two or Four or Nine will need to be added to the game to reduce Casters threat to crits.