Obi-Wan has lot of practical experience fighting dark jedi and Sith at this point, and is battle-hardened, whereas Qui-Gon - while a good jedi in general - showed in TPM that he did not have what it takes to overcome a crafty and patient opponent. His Ataru style is all about aggressive and direct assault without any real defense. Obi-Wan has a greater chance of wearing him out and exploiting a weakness.