In Kanto, I love Celadon City the most. It houses the huge department store, the mansion where you get Eevee, the Game Corner with the addictive slots and rare prize Pokemon (in addition to secret Team Rocket shenanigans!), and the cutest Gym Leader!
In Johto, I favor Ecruteak City. I love the music, the architecture, the Kimono Dance Theater, and the historical Burned Tower where you first meet the three legendary beasts. There's also the Bell Tower where you meet Ho-Oh and the Bellchime Trail with its lovely autumn trees. A very beautiful city indeed. Ecruteak reminds me very much of real-world Kyoto in Japan.