I think you slipped a cog or a link. Maybe it's just your nomenclature usage. You mention a chain in the header then you want to compare a shaft drive to a gear drive. A shaft drive (common term used when describing motorcycles) and a gear drive is effectively the same thing. A "shaft" drive is nothing more than two gears connected together by a shaft. Conventional chains (like a bicycle chain) use sprockets and sprockets are different than gears. Of course one could get the "shaft" and end up on the "chain" gang but that is different too.
Fungo