In my opinion, this entire Cena/Rock thing and especially the WWE Championship, may very well not be the focus of creative. It's not important to immediately fix these plot discrepancies, they have a lengthy amount of time to work with. With the absence of the Championship and perhaps even Cena (maybe even for a few months), this could be an opportunity to:
1) Push new wrestlers. Perhaps more and better storylines? Though I doubt it, Zack Ryder could get his own feud and his "Long Island Iced Z story." People we want might get the push they deserve.
2) Reaffirm the Position of Lesser Titles: Let's face it. The WWE has only had its real focus on the WWE Championship and the World Heavyweight Championship. The other titles have taken a backseat. With the absence of the WWE Championship Title, McMahon can decide to have MitB briefcases cross over between brands, promote the United States, Intercontinential, and Tag Team Championships. Hell, this and the signing of the Kings of Wrestling (a tag team from Ring of Honor) could mean that WWE has decided to focus on improving tag team matches, making them actually entertaining.
3) Dazzling the Stage: WWE has just shown off two men wrestling, and was one of the best matches in years, and by the drama and mainstream heat alone outshines even the Rey Mysterio/John Morrison match a couple years ago. With the opportunities ahead of them, WWE could have listened to those study groups they made of former fans and new fans and old fans and the IWC and decide to put an emphasis on in-ring ability, as it really does raise the roof as we saw in Chicago. We're tired of shitty, repetitive matches, and they now know it. Things can be changing for the better, and we might have great matches more often.
Biggest question is, how about WWE working with Ring of Honor? Punk's story could transcend promotions, and hold title matches in the Indy group.