First would come Goldenrod City. I've always had a likeness to the center cities (i.e. Vermillion City, Goldenrod City, Mauville City, Hearthome City). I like the fact that you know you'll visit it upon many occasions and it's centered around various cities, buildings, and other small yet major aspects of the game. In Goldenrod, you already have so much from the GTS, Bill, the Day Care, to the Name Changer, Department Store, and so forth. I don't think it's the best looking city in Johto, but it is a favorable one.
Next would come Blackthorn City; the last city and one of the best in my opinion. It has the Ice Path in the North, then the Dragon's Den behind the gym. It's also one of the spots with the higher leveled Pokémon (although, a majority of them being Graveler, eh). I think this is one of the most calming cities in the game, and also one of the best designed, but still not the best looking- which is very contradictory, don't you think?
...Best looking for me would probably go to Ecruteak City, but it isn't my favorite because that would go to my earliest mention.
