What are these spots for?

for your ingame house that you can purchase

>>28438600
this

it's secret bases 4.0

Where you build the gyms.

anal

>>28438571
Considering the proximity the the centers, maybe they are arenas with respawning trainers.

far left just looks like a platform for a dock where you'll meet some NPCs, perhaps scripted event for Team Skull

far right looks like just a grass enclosure that is typical of towns like in Kanto

bottom right is a body of water

top right looks like a blocked off area between routes

don't know about top left

basketball courts for the bball minigame

designated shitting squares