Megatron was chosen as Decepticon leader simply because he was the most expensive toy they were willing to release initially, which made him match Optimus being the most expensive Diaclone toy they licensed in the first year. Shockwave is technically taller, but was cheaper and had less parts(Megatron's whole scope and silencer set being equivalent to Optimus' trailer)
Interestingly, Jetfire and Shockwave would release by the end of 1984( but are counted as 85 toys), and both were bigger than Optimus or Megatron. They might've been considered leaders instead if they were licensed earlier- then again neither were Takara molds(and thus not released in Japanese G1) so that might've been unlikely considering the cartoon was made with Takara eventually airing it in mind(which is why Jetfire got made into Skyfire)
Still, it'd be interesting to think of a situation where Jetfire(or Blaster, who's also big and would've been available in 84 if they chose) might've been what we know as Optimus and Megatron. Of course by year two they dropped the idea that the leaders were the biggest toys.