In the currently running Energon Universe comics, Megatron is now a triple changer. At some point in time before he arrived on Earth during the war, Megatron was abducted by an unknown alien (implied to be Unicron working through a Quintesson servant) and put through a series of trials by combat. His original form was a tank, but after this trial he was gifted a third form, which is his iconic pistol alt mode. This new form grants Megatron the ability to "infect" the person who is wielding him, controlling them completely when held and implied to have lingering after-effects when not in direct contact. Even Optimus has experienced this corruption when he was grafted Megatron's cannon arm.

So in short the current comics have explored and played with the idea that Megatron favors his pistol form over his tank form because the former allows him to dominate those who use him.