I think the fact that the Ponds weren't real important to this story, and for the whole on-and-off-again nature of their recent relationship w/ the Doctor, serves a purpose. It's pretty obviously a set up for the next couple of episodes, where the silliness of this state of affairs ultimately leads to the Ponds opting to no longer be companions. (In fact, the toll of this on-and-off-again relationship is apparently the overriding theme of next week's episode.)
But why set up such a complex parting story, when countless previous companions have been pretty much abandoned with far less fanfare? I believe it's because while Amy and Rory are leaving Doctor Who itself, that they are still going to continue playing an ongoing role in the greater Whoverse.
When Liz Sladen died, BBC was smart enough to simply end "The Sarah Jane Adventures" rather than trying to recast Sarah or to retool a Sarah-less version of the show. But since then, I've heard that BBC has regretted not having a nice strictly kid-oriented Who spin-off in the CBBC line-up. And I seriously think (hope) they're maybe getting ready to fill that empty niche with Amy and the Last Centurion.