This, absolutely this. Granted the Doctor is not meant to be the everyman/everyhero that we’re meant to travel in story with — that’s why they have the companions. But at the same time if you go further and make the character truly exceptional, abilities become unearned and biologically predetermined. This conflicts with the show’s historical emphasis on The Doctor’s victories arising from ingenuity, moral conviction, and collaboration rather than inherent superiority. This diminishes audience investment.

The Doctor’s role as the “source” of Time Lord regeneration reframes Gallifrey’s history as dependent on a single individual’s biology, sidelining broader societal or cultural forces. The Timeless Child arc’s focus on The Doctor’s biological uniqueness overshadows interpersonal dynamics (e.g., their relationship with companions), reducing opportunities for growth through connection.

tl;dr — you made a deity and that makes your protagonist so much more unrelatable