There are several great reasons to run in Tokyo. It is safe and relatively clean. There are plenty of public restrooms. There are lots of riverside terraces (Tama, Sumida, Arakawa rivers). The train system makes it possible to run anywhere (just make sure you have a pasmo) so you don't have to follow the same boring path over and over.
One of the lesser touted pluses of running in the megalopolis is the endless sources of unusual things to look at. When you run 10 km (6.2 mi) or more, you end up going to places that you would normally never visit. Here are a few of the more silly and random things I've come across on runs around my neck of the woods lately.
Open the door to an exciting and challenging new future
Prayers only, no fakers that just close their eyes and stand there
"I go to GOOBER for all my live bait needs in Tokyo"
To be, and not to be? That's is a question