Because Cena still had that big move to pull out of the bag, Punk had already hit 2 GTS's and Cena kicked out of both, so he had nothing else of his own left to dish out, hence him going for a moonsault and the Rock Bottom, moves he's never used before.
Dunno, just thought it was only used as a way to have both guys shoulder's down at the end. I mean, why did they think Cena could even pull that move off. A middle rope bridging german suplex pin? Could Cena even do a normal german suplex bridge? It just looked awful imo, and they didn't need to risk the quality of the finish just to have both guys get pinned. Like seabs said, probably loads of other things they could have done without risking the quality and making the crowd not care. Just didn't like it personally. Like I said though, I absolutely loved most of the match, and they looked to be heading to their best match yet for the first two thirds of it.
I agree on the SS match being the best. Adored that match (MITB too, but the SS match took the in-ring work up a notch, and had the best finishing stretch last year imo).
He used the Rock Bottom a week ago on Raw, and not because he didn't know what else to use, but because it was a shot at The Rock. Punk hates Rocky, and he knows using his finisher against someone who already lost to it, like Cena, would irritate him. I don't remember fully, but I want to say Punk pulled out the Rock Bottom before he hit that second GTS.
Agreed with pretty much everything else, though. The finish was strange but I appreciated seeing both men use moves we haven't seen from them before. I've personally never seen Punk do a moonsault or Cena do a German, and now I know why. But still, it was fucking cool as hell seeing Cena, and Punk for that matter, trying new shit instead of going to the well again for the millionth GTS or AA.
In fact, I almost like how bad those off-arsenal moves looked. Cena doesn't ever use a German suplex, which explains why it looked awful. Punk never uses a moonsault, which is why it looked awful. They were each getting desperate -- as Cena is wont to do in big-match situations (see: WM28) -- so it's expected that those moves would look like garbage. There's a little more charm and realism to watching Cena struggle with a German suplex than if he were to just hit it perfectly. Now, THAT would have been silly.