I'm sorta surprised by your statement. I've lived in Seoul, Tokyo, and NYC for various periods of my life and I'd definitely say Tokyo feels the most "modern" when you scratch beneath the surface.
For example, I'd say the basic subway system between Seoul and Tokyo are pretty similar but you also have the advantage of a vastly superior rail network that serves Greater Tokyo and the rest of Japan. KTX and SRT in Korea are improving every year but don't really compare yet. Additionally, the new subway stations in Seoul are quite nice (Line #9) but you also have really old lines (Line #1) where many of the stations are so badly maintained they feel inferior to their counterparts in Tokyo (Ginza, Hibiya).
I can't really speak to the english speaking issues in South Korea, but in Tokyo I never really had any issues even though I don't speak Japanese. Most places in Tokyo will have english menus because it's a tourist centric city. Neighborhood family owned dives probably don't speak english very well but they wouldn't in Seoul either.
The thing that makes Seoul fall short for me is the standard of building maintenance. Although things are changing, it was generally the case that for several generations of building maintenance they just expected to tear them down and rebuild. Tokyo has a similar problem, necessitated by constant building damage and updated building codes from earthquakes, but the biggest difference is that a lot of these buildings in Seoul are 10+ stories tall. Most of Tokyo's building stock is <10 stories. It's become cost prohibitive in Seoul to actually tear these buildings down and rebuild them.
One of the worst things for me is how car centric Seoul is. It's rare in Tokyo to have 3+ lane roads that aren't toll road/expressways. They're all over Seoul and the side roads are packed full of "valet" parking for restaurants that don't actually have parking lots. The entire car culture feels way more chaotic there than Tokyo. In Tokyo, you can't buy a car unless you prove you have a registered parking spot. In Seoul, you just double park your neighbor and put your phone number in case you need to move your car.
Lastly the air quality in Seoul is way worse than Tokyo. Feels like you constantly have to stay indoors for weeks during the bad "yellow dust" season.
I have taken KTX but I have not taken (non-subway) rail in Japan. The KTX train I took was similar in quality to German inter-city rail or American regional rail lines. That is to say, it wasn't that special.
I think there are pros/cons of car culture and systems in both countries.
Japan's car-ownership experience is rather hostile. Expensive tolls, Shaken inspection, and higher price tags than SK. In a way, this benefits tourists because streets are cleaner, cars are newer, and people tend to drive less.
In Korea, it's flipped. It's great place for car ownership. But from tourists POV, it's chaos.
As much as I love Japan, I'd prefer to live in Korea while visit Japan as tourist. Seoul isn't so bad once you go outside from central Seoul to new cities. Everything is more spread out, cleaner, and very modern.
"Urban area" doesn't mean people don't need car for living. Maybe threshold of "urban" is too low than we think.
You're just a tourist so you may can't see everything, but didn't you saw many small/family cars run on Miyagi at trip? Sendai city in Miyagi, maybe ranked TOP 10 city for great public transport in Japan, 75% of family still buy at least a one car. Rest of the place is far worse than Miyagi for transport. Of course they buy cars becaues it makes sense.
I lived in sendai for 3 years, and I have lived in Seoul currently for 5 years. Sendai Station has a giant underground bicycle parking, the likes of which I've never seen in Korea.
There are cars in Japan, of course. Families own one because it's convenient, of course. Also there are more cars in Japan than Korea, mostly because more people can afford it. But I'm quite sure that, at comparable income levels, Koreans own more cars per capita.
Korea has a very car-centric infrastructure, and people own massive cars, and drive recklessly, because the roads allow you to and people are used to it. Children are taught to never cross the road if they see a car, no matter if they have the right to cross or not.
I'm not saying Japan is a car-free country, of course. But car culture and car safety is a lot more reasonable.
For example, I'd say the basic subway system between Seoul and Tokyo are pretty similar but you also have the advantage of a vastly superior rail network that serves Greater Tokyo and the rest of Japan. KTX and SRT in Korea are improving every year but don't really compare yet. Additionally, the new subway stations in Seoul are quite nice (Line #9) but you also have really old lines (Line #1) where many of the stations are so badly maintained they feel inferior to their counterparts in Tokyo (Ginza, Hibiya).
I can't really speak to the english speaking issues in South Korea, but in Tokyo I never really had any issues even though I don't speak Japanese. Most places in Tokyo will have english menus because it's a tourist centric city. Neighborhood family owned dives probably don't speak english very well but they wouldn't in Seoul either.
The thing that makes Seoul fall short for me is the standard of building maintenance. Although things are changing, it was generally the case that for several generations of building maintenance they just expected to tear them down and rebuild. Tokyo has a similar problem, necessitated by constant building damage and updated building codes from earthquakes, but the biggest difference is that a lot of these buildings in Seoul are 10+ stories tall. Most of Tokyo's building stock is <10 stories. It's become cost prohibitive in Seoul to actually tear these buildings down and rebuild them.
One of the worst things for me is how car centric Seoul is. It's rare in Tokyo to have 3+ lane roads that aren't toll road/expressways. They're all over Seoul and the side roads are packed full of "valet" parking for restaurants that don't actually have parking lots. The entire car culture feels way more chaotic there than Tokyo. In Tokyo, you can't buy a car unless you prove you have a registered parking spot. In Seoul, you just double park your neighbor and put your phone number in case you need to move your car.
Lastly the air quality in Seoul is way worse than Tokyo. Feels like you constantly have to stay indoors for weeks during the bad "yellow dust" season.