Cena's already had a "kryptonite," and his name was Dave Batista. Think about it: they came up at the exact same time on different shows(Cena on SmackDown, Batista on RAW) with zero interaction. They tied in The Royal Rumble 05, but ultimately in their first clash, Batista won The Royal Rumble, and won The World Title at Mania 21 while Cena won The WWE Title the same night. After the draft that year, these two had practically ZERO interaction(other than I believe a Tag Match at No Way Out 07) for about 3 years.
Then in 2008, after said 3 years of no interaction, Batista gets drafted to RAW, and in something that could only be avoided for so long, they started building toward a huge face vs face match at Summerslam. At Summerslam, they put on a kickass match with tons of excitement, but ultimately, Cena lost, and practically had his neck broken in the process.
Fast forward to 2010, you have a badass heel Batista and John Cena that start getting involved in the Bret Hart/Vince McMahon saga, which involved several grueling attacks and Cena, as well as promos consistently running him down, as well as a brief explanation of everything I've already explained above, with I believe the most notable line being "When you and I are in the ring, bad, things, happen." Somewhere between at Elimination Chamber, Cena wins The WWE Title, and Vince feeds him to Batista a few minutes later, and you easily have Mania's main event set had it not been for Taker/Michaels II: Batista, the ultimate bad guy, the man John Cena has never beaten one on one, The WWE Champion, vs John Cena, the face of the WWE, the one thing Batista could never take away from him.
Once again, they put on a kick ass match which was easily a Wrestlemania level show stealing performance(again had it not been for Taker/Michaels II) with drama excitement, and so much more(if you don't think it was a good match, there is no hope for you). And it finally happens, on the biggest stage of them all: John Cena finally defeats Batista one on one in the center of the ring via submission to win The WWE Championship in front of 72000 cheering(and booing) fans.
Then over the next few months, they have a Last Man Standing Match and an I Quit Match, where again, Cena comes out victorious(and deservingly so), and the night after Over The Limit, Batista quits(both in kayfabe and real life of course) and leaves the company for good, showing that John Cena has FINALLY gotten rid of Batista, the man you could call his equal for the 5 years they were both on top of the mountain, and ultimately, that's the way it should have been.
So yeah, in short, Cena's already had a kryptonite, and you could argue he had it for 5 long years, and as the face of the company, Cena overcame it. And at this point in his career, it'll be quite hard(if not impossible) to give him a "kryptonite" that you could argue is at his level. With Dave coming up at the same time, it was an easy argument, but now, I'm not so sure.