I would say that it is a handy plot device/storytelling tool for the writers.
Take the latest episode, Churchill rings the Doctor a month ago because he's not sure about the Daleks. If the Doctor had turned up immediately he would have had plety of time to stop their plan (perhaps they wouldn't have been built yet, perhaps they wouldn't have been in the same room as the Prime Minister or perhaps they wouldn't be ready for him). But instead he turns up and it all kicks off immediately. Much more exciting.
Similarly if he had popped back for little Amy after five minutes then his new compaion would't have had such an interesting back story.
So the inability to micro jump, just like the faulty chameleon circuit, the regenerations and so on are all tools for the writers to tell more interesting stories.
The writers don't write it into the story because the TARDIS is faulty, the TARDIS is faulty because the writers write it into the story. Whatever explanation they come up with (old model, needs 7 pilots, mid of it's own) is just a means to an end.