Tough question! The biggest challenge being that cramped stores filled with cheap items is sorta their “thing”.
There are a few “MEGA Don Quijotes” in Tokyo (https://jw-webmagazine.com/large-don-quijote-and-mega-donki-in-tokyo/)… but it doesn’t seem bigger means spacious, just “more room to put more stuff in”.
I know the one in Mizue was asked by a local disability group to keep the aisles clear and they did… for a few years but now it is becoming more like the others.
My only real suggestion is to use the pictures feature in Google maps. If you select a location, details show up in the information pane and if you scroll down there are often pictures from inside the store, allowing you to get a bit of an idea what it might be like to navigate.
I wondered if they might have wheelchairs available to borrow (as it would have a better turning radius) and it came up in the FAQ but the answer was just “it depends on the store, ask the store”… not super helpful!
Sorry for a not very helpful answer!