Adding Con to HP only at 1st level while increasing the overall amount of HP (by giving max HP per level) seems like a decent idea. But I'm not sure it's enough:
Ftr 20 with Con +6: 206 HP (new system) vs 234 (default 3.x)
(Theoretical) Mage 20 with Con -1: 79 HP (new system) vs 31 (default 3.x)
The fighter still has way too much HP. The Mage is, indeed balanced better. But is the low Con penalty enough? I'm still tempted to add that Bleeding penalty for negative Con.
The Simulationist inside me can accept adding Con to AC, perhaps as a Natural AC bonus. He's iffy on adding Con to Reflex saves, though.
"Soft" DR against natural hazards and such is something I'm already using, though it's a bit difficult to adjudicate properly.