Samus travels in a very fast, very nimble spaceship, and has a power-suit able to move at super-sonic speeds. A motorcycle is... a bizarre choice. Unless you're thinking first of merchandising.

Samus can turn into a ball and literally roll around everywhere she needs to get on the ground, so she doesn't need a bike which would actually have less mobility since it can only ever move forwards and backwards as well as not fit through spaces Samus already squeezes into when in ball mode.

She also had a spaceship, so she really doesn't need a bike to get anywhere else.

also, a motorcycle is a vehicle for urban travel

I'm not aware of any Metroid games set in an urban area

spez: also motorcycles require roads and Metroid games are set on undeveloped alien planets