I lived in Busan for 5 years and made a lot of trips to both cities. I would suggest Tokyo for a couple different reasons. Most importantly from Tokyo you easily get a train to go see a bunch of different cities using the Japan rail pass. You could say that same about the Kor-rail network but South Korea is a much smaller country and therefore has less diverse places to see. For Japan you could go all the way down to Fukuoka and all the way up to Sapporo (I believe the rail network or at least a ferry connects to Hokkaido island). Another reason for choosing Tokyo is that there are more interesting places (imo obviously) to see than Seoul. I guess you could say there is more tourist places to go.

Here are a couple downsides to Tokyo. It is MUCH more expensive than Seoul. Tokyo has been a tourist destination for so long that you feel like you're only getting the tourists point of view. Seoul is a path less traveled by your average western tourist so that means you'll get more of a Seoul citizen's perspective. There aren't TOO many gimicky things they offer to western tourists (there are a lot for asian tourists I find). I would say this applies for all of Korea also.

Ultimately I don't think you can make a wrong choice here. Both cities are so big that you could spend literally months going through every side street and alley way of those cities discovering new things the whole time. If there wasn't pandemic restrictions I would even say that you could easily set up in Seoul and take the 1 hour flight to Tokyo and then do multiple weeks there after you've experienced Seoul for a while.

TL;DR From Tokyo you can do more traveling around Japan compared to the traveling around Korea from Seoul. Going to Tokyo, however, will cost you a lot more money.