Naruto said that big techniques aren't of any use against Kaguya. The only "big" technique that could be useful against her was the Nine Bijuu Rasenshuriken he used, and only because they targeted her "weak point" by causing her Bijuu chakra to become unstable. Naruto knew the whole time that the only chance against Kaguya was to seal her.
Against Sasuke, the whole fight was a clash of big attacks, so Naruto needed to gather as much chakra as possible to create a mode that could fight against Sasuke's Susano'o. The strategy was student; unlike Kaguya, Sasuke can actually be harmed by attacks, so Bijuudama are useful.