Cheap way for daily commuting in Japan

I'm traveling to Greece and plan to do a PhD in Japan next year with a MEXT scholarship. So I am looking for an expense report while I go there.

As far as I've heard from public transport, rents in Japan are on the roof compared to rents in Greece. So I decided not to use public transport, but to use a 50 cc motorcycle for daily commuting between home and university and back.

But I want to know if this is a good idea. The particular scooter I think is the Honda Supercub because it's easy to maintain. Is the small motorbike recommended for daily commuting in Japan?

My goal is to save money while staying in Japan for a long time (I estimate 2 to 5 years).