If we're not restricting it to the games, LaRousse City and Altomare are my two favorites, and two I'd really wish we had the chance to explore in the games. I also liked the anime's version of the Seafoam Islands much more than the games', since it was a resort town rather than a pair of caves.
Just as far as the games are concerned though, my two favorite cities are Goldenrod and Nimbasa. Goldenrod felt like a true major city (unlike Celadon and Saffron, where you couldn't even enter most buildings), including almost everything you can think of either in, or right by the city. As for Nimbasa, it had quite a bit to offer as well, but didn't feel as busy as Castelia, which was almost too big.