The Doctor shrunk back into the recesses of the TARDIS' door frame, wounded by the words. She'd come to see the TARDIS, but not him? His insecurities were confirmed - despite the joking and flirting going on over the network, Rose was uncomfortable being around this new regeneration of his.
The features of his face softened, and he frowned. "I see." Pause. "What do you think? Changed a bit since you last saw her." Another pause. "You probably don't want to peek inside. It's really changed, in there," he said, tilting his head in that direction.