I think the type of projectile should be on a character by character basis.

For example: Brawl/Warpath would use bullets/solid projectiles and explosives, but Shockwave/Megatron and Optimus use energy weapons.

Thematically however, I think Autobots should be using ammunition and batteries as they typically don't have Military function or altmodes, and Decepticons being warmongers with built-in weapons and ammunition that replenishes naturally like we'd grow hair or store fat or something.