Federer will never ever again play like he did in his prime, this is obviously clear to everyone I hope.
What I think the main difference is, that he learned to play with a lot more brain & effectivness than with power shots. This sounds ironic since Federer isn't a ball basher, but I remember many matches in his prime where I thought he's just going for the winner because he can and probably still make the point/winning the match, not because it's the most effective shot.
Right now I think the variety and the intelligent way to construct a point, outplay an opponent and using his whole arsenal of shots he can do makes the difference.
A guy like Tsonga would've never troubled Federer in a GS-QF in his prime, just because he could not have outpowered Federer in the rallies the way he did today. The losses against Soderling, Berdych, Tsonga and Del Potro are the best examples for that kind of transition.
Guys like Gonzales never stood a chance against Federer 5-10 years ago, whether their game was on or not.
"I'm better than most of the guys here in tennis and I'm also smarter than most. This justifies my sometimes cocky behavior." - Maximagq