I have to disagree very strongly here.
Not so long ago I spent a couple of weeks in Tokyo as a wheelchair user and this smashed my own preconceptions.
I'd also assumed that there weren't that many wheelchair users - odd thing, is that once you're using one, and using the same routes and paths to the trains as others in the same situation, then you realise how many there are. I hadn't noticed any before that trip, but I can assure you there are plenty.

There are more stations than not within Tokyo that have wheelchair access, and even those that don't appear to have access (such as Shinbashi) might have facilities (like this one showing yours truly exiting Komagome station). My understanding is that every station on the Yamanote line can be accessed by wheelchair.

There are some areas around Tokyo where access is poor, but these are actually few and far between.

Having come from London, Tokyo was a liberating experience for me. Access to Toei Buses was first class, most of the train/subway system was accessible, and getting around on the ground was, mostly, a breeze. As well as plenty of conventional wheelchairs, I saw a few electric ones also. Passengers using these were able to travel by train unescorted - a member of staff would accompany them to the platform, a yellow ramp was unfolded to help get them onboard, and the passenger was greeted at their destination by a waiting member of staff with another ramp. This service was always offered to me, but was never needed. I saw people in heavy electric wheelchairs being assisted onto a train three times in those two weeks, and I wasn't using the trains heavily.

Hang around the elevators at Shinagawa station, and within an hour you should start seeing your first wheelchair users. Just slow down, look down, and open your eyes.

Tokyo is a fantastic place to go as a wheelchair user (Rome, now that's a nightmare, nevermind the thousands of elderly and lame visitors who go to the Vatican ) that's why it's particularly shameful when places like Toyoko Inn undermine this extraordinary effort to make it so.