This is something that's always gone over my head.
If we are to say that from the very episode back in the sixies to the end of this year's fifth season, and not counting the time between the end of the "1996 Movie" and "Rose", we have pretty much been with The Doctor from the get go, then how could have aged (in Earth terms) any more than 40-50 years.
I'm not familiar enough with the original series to comment there, but there's already been
plenty of breaks in the Ninth, Tenth, and Eleventh Doctors' chronologies for him to have ages and ages of unchronicled adventures.
To start with, we have no idea how long it had been before meeting Rose since the Eighth Doctor regenerated into the Ninth.
In "Rose," we have no idea how much time passed for the Doctor between the TARDIS dematerializing and then rematerializing, with the Doctor leaning out to say, "Did I mention that it also travels in time?"
We have no idea how much time passed for the Doctor between Rose's becoming trapped in Pete's Universe and the Doctor using a supernova to send one final goodbye signal into the alternate universe on Christmas Day of 2007.
We have no idea how much time passed for the Doctor between "The Runaway Bride" and "Smith and Jones."
We know that the Doctor spent three months impersonating John Smith in 1913 England, and we know that he and Martha spent another three months living in 1969 as a result of the Weeping Angels in "Blink." And we know from "The Infinite Quest" that he was at one point separated from Martha Jones for three years before reuniting with her.
We have no idea how much time passed for the Doctor between "Voyage of the Damned" and "Partners in Crime."
And, of course, we have no idea how much time passed for the Doctor between "Journey's End" and "The Next Doctor," nor between "The Next Doctor" and "Planet of the Dead," nor between "Planet of the Dead" and "The Waters of Mars," nor between "The Waters of Mars" and "The End of Time, Part One."
And we have no idea how much time passed for the Doctor between his disappearance after defeating the Atraxi and his reappearance in Amy Pond's garden to offer her the chance to travel with him.
Although we can leave some time between episodes, It's fair to say that Rose traveled two years with the Ninth Doctor, not five;
I'd put it closer to one year, myself. I figure she probably travelled for one year with Nine and one year with Ten.
Well, depends on how you're counting the Year That Never Was. We know she travelled with him for at least six months between their getting stranded in "Human Nature/The Family of Blood" and "Blink." "Smith and Jones," "The Shakespeare Code," "Gridlock," "Daleks in Manhattan," "Evolution of the Daleks," "The Lazarus Experiment," and "42" all seem to take place, for Martha, more or less one right after the other. And we have no idea how much time passed between "The Family of Blood" and "Utopia," though we know that at least three months were spent in 1969 and there was some unchronicled adventure during which the Doctor and Martha encountered Sally Sparrow (at the end of "Blink"). I'd guestimate that Martha spent at least seven months with the Doctor, and of course a year traveling the world to spread the Doctor gospel, before leaving the TARDIS.
Hell, even the first few episodes of this years series came one after another, so there is no gap between them.
Well, we really don't know how much time passed for the Doctor and Amy between "Victory of the Daleks" and "The Time of Angels," nor how much time passed between "The Vampires of Venice" and "Amy's Choice," nor between "Amy's Choice" and "The Hungry Earth." We can probably assume it's been a relatively short period between "Cold Blood" and "Vincent and the Doctor," though, as Amy's remarks that the Doctor's been unusually kind to her seems to imply this is a new development.