Wow some huge changes there. I love hex games, but then I'm not sure I want my hex war games mixed in with my civ game. I agree that stacking was just stupid, but there needs to be some way to mass forces without bulding generals to build armies. In the end unless the game changes to a full war game, you'll essentially stack units laterally and it'll still come down to who has the biggest pile of guys.
I can't say I'm looking forward to the finite resources thing. Seems like we'll just become scavengers now waiting to ambush a unit to get whatever it drops. Seems to favor turteling since you can just take whatever the invaders drop to increase your forces. I didn't really like religion in the first games, but it seems kind of retarded to get rid of it entirely. Just for the story of the game, having the various nations sort of drawing the lines against each other based on religion increased the realism and enjoyment for me.
Everything else looks good though.