That's right. 2013 was clearly for Rafa IMO. Novak and Rafa were tied in Slams on hard that season, so their Slam H2H is the immortal tie-breaker for the colective memory of posterity. When tennis fans think of 2013, the Roland-Garros 2013 SF and the US Open 2013 final will be the first thing that will come to their mind.
Grand Slam achievements > achievements outside Grand Slams.
Therefore, while Novak did win Beijing and the ATP finals in dominant fashion (beating Nadal in the finals as well), it was quite impressive, but simply not as relevant as the US Open final due to the aforementioned logic (Grand Slam achievements > achievements outside Grand Slams).
I'm not aaying Slams are all that matters, but they're the most relevant metric. In case two players are tied in Slams achievements, other merrics can be used as tie-breakers. But, they weren't tied in Slams achievements on hard in 2013. Nadal winning the H2H in Slams on hard gives him decissive advantage. When people think of the 2013 comparison on hard between Nadal and Novak, the first and most relevant thing that comes to their mind is the US Open final.
Also, Nadal winning the North American Golden Tour (Cincinnati, Canada and the US Open), a feat very few players have achieved in the history of the game, and beating Novak twice in the process, was pretty epic
Indian Wells too. Simply too much.