Anything that has lasted as long as Doctor Who, has had as many show runners and writers, won't fit together neatly like a puzzle.
We're not talking about stories from multiple showrunners decades apart though, are we? We're talking about a story from the same person only a year and a bit later. No one forced him to have Amy and Rory's last stories take place over the span of a decade but since he chose to do that he shouldn't then ignore it because "most people won't notice". If that was the only reason for ever doing anything the world would be in an even worse state than it already is.
But as we see, people will pile on RTD for any tiny inconsistency while jumping through hoops to forgive any of Moffat's blunders.