Summary: He may appear physically weak thanks to the Master, but the Doctor is still strong enough to defeat him.
The Master would call the Doctor’s interest in, and his fondness for humans a weakness. Perhaps from his point of view it is, but then the Master doesn’t let himself grow attached to anyone or anything. That’s the fundamental difference between them: the Master cares only for himself, his needs and desires, while the Doctor cares about all the wonderful and varied forms of life that populate the universe.
While the Master’s busy tearing everything apart with his paradox machine, the Doctor only wants to put everything back the way it was.