hmm... I'll divide them by region
Kanto - Fuchsia City (gotta love that zoo and safari zone but nothing beats pallet town with the nostalgia music)
Johto - Goldenrod City (the train and the radio towers were the highlights of johto. alongside that underground thing)
Hoenn - Mauville City (hoenn's one of my favorite regions, only second to unova and it's difficult to decide >.<; i'll go with mauville from ORAS. many people hate it since it "ruined" mauville and it was a "copy" of Lumiose. but eh, it's good for me and made the place more interesting).
Sinnoh - Canalave City (the library and the bridge are the highlights. along with the antique feel of the whole city)
Unova - probably every place hahaha (unova is my favorite and every place has good music. there were times where i stayed at village bridge just to hear that music. but there were times where i also stayed at anville for that quiet environment and very nice music. but if I had to pick on the fly, I'd go with Castelia City. it's because of Skyarrow Bridge and the fact that castelia was said to be based off of new york)
I don't have favorites for Kalos and Alola yet :(
I haven't replayed them too much to decide haha