Tokyo and Osaka weren't mentioned in the same exclusion as London and Paris, but they each have many convergent points.
While Shinkansen services converge on Tokyo station, JR East limited express services terminating in Tokyo also do so at Shinjuku station on the West side of the city and a handful at Ueno in the north. Most JR commuter services will pass through either Tokyo/Ueno or Shinjuku. Private rail operators have their own stations at Shinjuku and Ueno, and additionally terminate some services at termini in Ikebukuro, Shibuya, and Shinagawa, with others running through metro lines in a manner akin to Thameslink or the Elizabeth Line.
Osaka has multiple traditional European large railway terminals at Umeda, Namba, Tennoji, and Uehommachi. There's also a smaller terminus at Yodoyabashi.