Long post Mr E! Regeneration is an uber powerful ability, as demonstrated by one villain (Kraken, a Doc Oc type guy) and one hero (Mr America, 100% idiot paragon) from our old game. If you're in a fight with someone and they have regeneration and your only ability is to attack them physically, ugggh, what a grind.
Personally I don't like the regen every other round just because I tend to lose track of the rounds, that's just my mental malfunction. I think going the 2d = 1d regeneration is a good way to balance it out.
One other option, could have Regenration be something the user has to roll every round. For every 6 they roll, they heal 1d. It would be a action unless they take a 1d boost to make it a free action.
Hmmm, something to ponder.
I like the Reconstitution boost. I wonder if Mental Regeneration should be its own power, rather than having it as a boost?
Good stuff, I'll mine the rest of your post later