I somewhat agree but I believe that Choji's experience in combat with his teacher changed his confidence problem. He decided to man up and do what had to be done - now he can fight people as close to him as Asuma and is brave enough to fight off Gedo Mazo, so I don't think he's going to panic against most opponents anymore.
On a side note I believe it's more fair since Choji doesn't use BM every battle, so it would be more like comparing base Choji vs. Shikamaru. Still, Choji's shown to be pretty powerful in base against opponents like Jirobo, so if it's Shika vs Choji than Shikamaru probably won't get his prep time. Remember that he's known to crouch in a position just to signify he's thinking. He usually requires prep time for his greater plans.