>>45017668You're partially right, the blue circles are planned towns. The reds in the back are simply very heavily WIP (making new tiles for them before continuing).
The ones in the front are indeed a bit empty. I've been rethinking a few of them already.
>>45017672This is done with Pokémon DS Map Studio (PDSMS), a relatively recent tool made for gen 4 and 5 romhacking. It's designed to work in tandem with SDSME.
