Kakashi couldn't control his MS well at the begin of shippuden and because of the lack of DNA, he couldn't fight for very long. He was still overall better than Sasuke at the begin of Shippuden, but Sasuke surpassed him when he absorbed Orochimaru, only because of his resilience and Oro's power, but MS Sasuke who fought Killer-Bee after losing Orochimaru's power became weaker than Kakashi. Kakashi on the other side was evolving(especially with his MS). Only after the fight against Danzo did he surpass Kakashi again. He received EMS, so evolved again, but at the moment he can't control it well, so he is basically the same as his older version against Danzo, with more stamina though. Kakashi on the other hand mastered his kamui on another level even able to warp Bijuus, warp himself/close range, warp things back from the kamui dimension, so much more evolutions which make me believe that he surpassed his student again. But it's obvious that EMS Sasuke after controlling his powers will be stronger