I assume we are counting towns, not just cities, so Lavaridge, Fallarbor, Dewford etc. can count?
Personally, it's a toss up between Sootopolis, Dewford and Slateport.
Sootopolis is really unique, being inside a flooded volcano crater. It has brilliant theme music, and quite a bit of mystery, what with the Cave of Origin, that house with the tress blocking the doorway, and the fact that you have to use Dive to get in there. It's based on an area outside of Japan too - Santorini, which is a flooded Caldera. That's why it has the different houses. Although if they had blue roofs like the ones in Santorini, it would just be even better. It's also the site of an epic battle between Kyogre and Groudon, that actually has cutscenes! (The only ones in Gen III, if I'm right). That place would just look godly in a remake.
Dewford has very little to do. However, due to the toughness of Brawly, I always end up spending a decent amount of time there. The music is really just the best in the region as far as I'm considered - it's so relaxing, yet it does reach a climatic point before sinking back down into the normal part. The town itself looks brilliant, being built on a beach - sand instead of streets. And the novelty of making those people in that house saying any combination of words in your vocabulary is cool too.
Slateport has some happy memories, as for the first ten or so playthroughs of Emerald I could never get past it. I don't even know how, because I always was blocked from entering the museum, yet I talked to Dock too. It has some good music, the market is cool - you don't have them elsewhere, unless you count that one in Driftveil in Unova, which isn't as cool. There's a Battle Tent, probably the second-best out of the three available, the museum has good music, and the beach on Route 109 is cool too. You can also get Minun just north of Slateport, which is awesome.
So...actually, I really can't decide. I get to Sootopolis less often, and it's got a brilliant concept, Dewford is so lovely, and Slateport is the accessible one with stuff to do. If I have to give an answer...Dewford, just to be different :)