Tokyo certainly isn't ideal for those with mobility problems, but now that you're moving around Tokyo, look at the sides of some of the stairways in the stations. Many have folded up apparatus that are used to carry wheelchairs and are actually stair lifts (note that they aren't for you to use!) Other stations have elevators, especially the newer ones, such as those on the Toei Oedo line. Anyone can use these, but they may not be obviously apparant.

A disabled person would have very similar issues using public transport as someone in London or Madrid. Some platforms/stations are accessible, some aren't. I'm sure disabled Tokyo residents are aware of which routes are possible, and which numbers they'd need to call to arrange for a station emplyee to work the stair lifts for them.

EDIT: I TAKE THIS BACK NOW. TOKYO IS EXCELLENT FOR THOSE WHO NEED TO USE WHEELCHAIRS. IT'S NOT PERFECT, BUT IT'S SIGNIFICANTLY BETTER THAN LONDON AND INFINITELY BETTER THAN ROME.

Almost forgot - don't forget to look down when you're in the transport network, all those yellow lines and bumps are there for people who have visibility problems.