I wouldn't call Rome 2006 a choke, or any of his losses prior to that choking either, Nadal was just better than Federer on those days. Federer got broken at 4-4 in the third in Dubai, was outplayed in Monte Carlo and RG.
But Rome 2006 was where it all started. It wasn't just the match points, there were many opportunities in the fifth for Federer to win it. 4-2, 40-30, if he wins that point/game he'll serve for the match, the match points, 5-3 up in the tiebreaker.
It was all there for Federer to take that match and he blew it. I think after that he never really believed he could beat Nadal again, at least on clay. Then after Wimbledon 2008 you started seeing it more on other surfaces.
I believe, like others do, if he had won in Rome 2006, the h2h would be different. It sucks, but that's life.