I think Nadal has a few very tiny weaknesses that don't often get mentioned. To clarify on this, I'm not saying these are his only weaknesses, or that his weaknesses are only small, but we all know what his major weaknesses are and so does the ATP tour. Instead, I'm talking about the little stuff that often goes unnoticed.
For instance, it's generally accepted that slicing against Nadal is a bad idea, and with good reason. No player makes a mockery of the slice like Nadal does. However, he only does so when a slice is either A) to the middle of the court or B) to his backhand side, where he uses his incredible footwork to run around it and pretty put the ball wherever he wants. What he doesn't do as well however, is handle sharp, low cross court slices to his forehand side, especially on faster courts. He struggles to redirect it up the line (he'll often either over-hit it, or dump it at the net), and he if he goes cross court, he can only "lift" it back up and roll it into play. Grigor's game is reliant on the slice so I understand why he kept playing them so much (but only to an extent, since you're still supposed to change your game based on your opponent), however, he should have gone with them to Nadal's forehand, for the most part.
The other weakness -- and one that Dimitrov did exploit fairly well, to his credit -- is Nadal's difficulty in handling slower high bouncing kick serves (mainly 2nd serves) to his forehand side. Because he doesn't step in and take it on the rise, he often hits the forehand at well above shoulder height (ironic, I know), and shanks it.
One thing I've noticed about him as well throughout the years, is that when he does opt for a backhand slices, he will often miss the subsequent backhand if he reverts back to the two hander. It's really curious, and I don't it's the change of grip that breaks his rhythm or what, but it's amazing how often it happens (though there weren't notable instances of this in this match).
Anyway, good win for Nadal, as he continues to look quite sharp.