It has better toilets, infrastructure, newer trains, much bigger (thus stations are almost always nearby), and integrated as a system as opposed to multiple metros in Tokyo, and so on.
Better toilets? When was the last time you came to Tokyo? Just before a bunch of big international events leading up to the Olympics, there was a crazy (re-)building boom for public toilets. And, if I know anything from experience in mainland China, their initial build is "wow" and (lifetime) maintenance "sucks". The public toilets will stink like most big cities in China after a couple of years. Where as Japan will put incredible effort into maintaining their public toilets.
Newer trains? Yeah, sure, because the network is newer. I can recall riding the maglev in Shanghai from the airport. The first thing that I noticed: The seat covers were filthy. So typical mainland China.
"[M]ultiple metros in Tokyo"? Use the Suica/Pasmo payment card. Hardly anyone thinks about what operator they are riding in 2023: They are thinking about destination and convenience. And, be real: The reason why Tokyo has so much complexity is the age and history of the system. (London, Paris, Berlin, and NYC have similar stories.) If Shanghai was rich in 1920 (well, it was, but that wealth was controlled by colonialists) and building metro lines, it would surely look different today.
Better toilets? Seriously? The toilets in the Shanghai Metro (or in China, in general) are among its worst features. Many are quite dirty and smelly, and most, if not all, lack soap and toilet paper.
Regarding infrastructure, yes it's new in Shanghai, but new != better. For example, the station floors may look shiny in Shanghai, but they become quite slippery on rainy days—a non-issue in Tokyo. Another example is that many trains in Japan have different air conditioning in different cars even within the same train, a subtle but welcome feature for those sensitive to temperatures—no such thing in Shanghai. Lastly, unlike Japan, metros in Shanghai/China still lack public timetables in 2023. A timetable can save you a lot of time by allowing you to plan your trip.
I agree that the integrated metro system in Shanghai is better for travelers.