First you have two questions here. The first regarding circumstantial analysis about when to punt and so forth. ESPN has done many simulations on when the computers say you should punt, kick, or go for it. To summarize if I remember correctly it was basically go for it until it is over 4th and 10 past your 30. Inside your 30, punt on 4th and 5 or longer. FGs were a trickier stance because you have to look at chance to make a FG but then % you will get the first down and also score a TD. Basically kicking on 4th and 5 or longer and maybe allowing a few more yards for longer FGs. On [ESPN Greg Easterbrook][1] has had a lot of simulations. As you said punting leaves lot of potential points on the table according to the analysis.
Again the sabermetrics in football are all over the place. KC Joyner has some and I laugh when I see some of his stats and some of his stuff is great. Football Outsiders does some advanced metrics too. This isn't baseball though. One guys trash could be another guys treasure because they are in opposite schemes and have different wants. So I think some of the advanced metrics will show up on more sites but really the numbers that matter are how you are grading out in-house.
Addendum: Thinking about this I had an extra thought. First I would like to accept my pro-don't-punt bias since I have coached for years and feel like my play calling forms an advantage (but don't all coaches feel this way?).
The point that I didn't include in my analysis is time. I find that most people compare these types of situations as to being at a blackjack table. If you have a 51% chance of winning when hitting on 16 you should always do it. But if you are sitting at a blackjack table you have unlimited time.
During a football game if you are on the wrong end of a few of these situational outcomes early in the game your team is behind the 8-ball. So if you find yourself down 28-7 at half instead of 14-7 based on two fourth down fails your game plan for the second half is much more limited. The defense knowing that you have to pass more is at an advantage.
So going back to the blackjack example it would be like saying you will always hit on 16 but after 1 hour your odds of winning on 16 is 40% per hand. The time factor is a big deal for teams with more talent. They don't want to shoot themselves early in the game when they know they have a better than 50% chance of winning every drive. A team that lacks talent could definitely use a higher scoring deviation to increase its odds though.
[1]: http://sports.espn.go.com/espn/page2/story?page=easterbrookpreview/070904