So, I remember a moment after River Song first regenerated into the River Song we know and she said, "Maybe I'll take the age down gradually over the years, just to freak people out." I guess it's possible the apparent age of a Time Lord is an expression of their mental state, something they can control with enough mental discipline, but something that might slip into old-old age if they're feeling really down and depressed. That's kind of stretching for an explanation, though. At the end of the day, the writers just wanted the Doctor to feel old so they made him up to look old. I have to admit they did a good job with it, and Matt Smith did an excellent job of ACTING old and tired. It still bugs me though.