For what its worth, I thought Del Potro's level was higher in this pretty great final. Federer wasn't at his best, but as usual gutted out a pretty impressive performance and had some shots at winning (DP hit some amazing shots to steal the win at the end).
Regarding the choking business. I've said it before, but its pretty silly, and worse likely missing something important. To see this, imagine you play random computer tennis between two identical cpu AIs in some computer game. On average you will see a 50-50 distribution of wins vs losses if its coded properly. Sometimes, but not often they will have blow out wins and blow out losses, just based on random chance.
Now improve the stats of one player so that all his attrributes ( forehand, backhand, serve etc) are better than the other player. All of a sudden the win percents gets skewed. One guy now wins a lot more than he loses. Moreover, when he wins, it tends to be blowout victories, but when he loses it tends to be remarkably close. (Mathematically you have two gaussian curves, that are shifted relative to each other, and one analyzes the edges of the distribution to make a statement)
Sound familiar? There is a strong selection bias at play with Roger Federer and some of these 'close' defeats. Notice that in almost all of them, you would say that the overall level of the player that defeats him tends to be higher. It's not like he's losing many matches where he was consistently outplaying the adversary (those tend to have different scores).
What's happening here is that we are judging his clutchness based on a biased sample. You don't include the many matches where he runs away with it in the 3rd set. Indeed his career statistics for tiebreakers, and deciding set victories (both 3rd and 5th set) are all really excellent. But again, one tends to focus on the few matches that seem to go poorly for Federer, and of course we remember them b/c they are unusual (here you can write down a finite list, starting with the AO 2005 and so forth). In some sense, that's to be expected with a player like Federer, who does so many aspects of tennis, a little 'better' than everyone else.