If you take both their careers up until Nibali's sudden vuelta win it never looked like Nibali would be better or become better. And the moment when Gesink became pro (2007) he did better in most times they met until 2010.
nibali is ofcourse 2 years older and 2 years longer professional, and a better bike handler. The last part explains 90% of the difference in results. Nibali doesn't fall, Nibali can make up time in descends when he is dropped (like Giro last year), and can put opponents under pressure before the final climb or when the finish is in a descend. And most of all, because Nibali doesn't fall he has rode and finished much more GT's than Gesink, a few times 2 a year, so Nibali has built up a lot more 'fond'.
It would be good if Gesink finished Tour and vuelta this year, just to catch up some of that 'damage'