Some of my favourite towns of Johto are Goldenrod City and Olivine City - the first, because of the great amount of things to do and to explore, and the second mainly because of its position near the coast...
A settlement where I'd live in, however, could be Cherrygrove - while it's easy to forget about this place later on, I actually like its music theme and all of those flowers. And it's the smallest city in the world, apparently.
to be honest, though, I found Sinnoh more interesting than Johto overall.