Tough decision for me.
While Christian/Orton was a straight-forward, classic feud that put on great matches and gave us a twist that we've never really seen before, CM Punk/Cena's feud constantly evolved.
Christian/Orton all stemmed from Edge's retirement and gave many long-term fans what they had been begging for... a Christian title run... only to have it taken away in a matter of a few days. When no one thought it was a good idea, it wound up resulting in some killer matches and skyrocketed Christian into the main event. WWE took a strange path to Christian's rise but it was absolutely effective.
CM Punk/Cena began with another failed Nexus angle but constantly elevated itself and improved. It allowed Punk to break away from carrying factions and shine on his own while simultaneously keeping the faction members that he left behind still relevant. What followed was a constant evolution of not only Punk's character but the direction of the WWE's way of producing pro-wrestling. His promo shook up the world and chain reacted into many important events that occurred this year: The epic countdown to Punk's contract expiration, Punk's seemingly impossible win at MITB after an easily five-star match-up (an match of the year in any promotion), walking out with the title, thus causing a title win for Rey Mysterio, losing that title to Cena on Raw, causing a Punk return for another epic battle with Cena at Summerslam (world title vs. world title which was never done before), only to have Punk win and Del Rio cash in his MITB briefcase.
So, the Cena/Punk feud resulted in FIVE championship title changes, four title reigns (regardless of length,) the promo of the year (Punk's shoot,) the pushing of two stars into the main event (Del Rio and Punk) and a partridge in a pear tree.
So yeah, as much as I loved the Christian/Orton feud, Punk/Cena did more for wrestling this year than any other rivalry and they get my vote.