You highlighted one result and made it as example for the whole season, and it isn't. First off, Isner is not a mug, just as Tipsarevic if we're being honest. Second, Nadal lost 6 finals of big tournaments and won Monte Carlo, Barcelona and Roland Garros. He also lost Tokyo final against Murray. Sure, result wise it was not a good year for one of the greatest, but if it wasn't for Djokovic, it could have been one of the best seasons in his career.
About Djokovic 2012 and 2013, hell yes they were peak years. In 2012 he played 17 tournaments and in 15 of those he was at least in SF. Sick. Won AO, Miami, Toronto, Beijing, Shanghai, ATP finals. Lost in QF of Madird against Tipsarevic and 2nd round of Paris against Querrey.
In 2013, he won AO, Dubai, Monte Carlo, Beijing, Shanghai, Paris and ATP Finals. Lost in SF of RG and in finals of W and USO respectively against Nadal, Murray and again Nadal.