I can't think of any inherent reason to prefer one over the other, maybe others will. If the points work better for you to start in Tokyo, I see no particular reason to fight against that.

Balance between the two cities is heavily dependent on your interests. Tell us what you hope to get out of Japan and we can converse on the topic.

Especially given that there is time, I highly suggest getting a guidebook from a company that you usually like, and starting your investigation there. I think we can help a lot in crafting your itinerary, but need first steps on your part to get pointed in right direction.

Luggage: there is a cheap luggage transport service that you can use to get past the luggage issues, but it does take a little bit of planning ahead (not much) since it is next-day rather than same-day delivery.