Having the Doctor staying with them is… well, it’s not that Amy and Rory don’t want him there, he’s their friend, it’s just that he can’t sit still for five minutes, always has to keep busy. Everyone else has to be patient, waiting for the mysterious cubes to do something, anything, but the Doctor doesn’t do patience.
It’s maddening, but even Rory can’t deny the Doctor’s trying to be useful, some of the time anyway. He creosotes the fence, mows the lawn, does the vacuuming… He’s both the best and the worst houseguest ever.
But he does make excellent waffles.