I think we should look at Pokemon Mystery Dungeon: Red and Blue. I always thought some of the friend areas would make excellent map choices.

pedoshark bluff from sky is where its at

Crystal cave / Fairy Tree -Saik

Huge Mountain / Flying Islands / Underwater City / Underground maze / Underground cave with a lake and giant tree -me

underground everything because this is TMNT pokemon edition

SANIC UNDERGROOOOOOOUdon

I believe we should have an urban area (albeit unpopulated because lol) for both more comfortable accessibility to things like Rotom and Pokemon that just generally live in those places (Eevee for example) - it could also give way for a Magearna quest if it's more of an advanced civilisation - even have a less technological and more religious area nearby for Pokemon more suited to that.

Another addition should definitely be another forest area in addition to normal but more scarred and gloomy - for dark, type and fire types without directly involving any haunting or fires etc

I woulnd't mind the idea of a city but i would wanna keep it a distance from stuff like villages as to not ruin the atmosphere of them by having a city of skyscrappers in the background.

Ancient/Sunken ruins underwater would be nice cause huge sea

Floating city like a city of bamboo or so like in pokemon ranger or co

or gold island(an island with trees and city out of gold that appears once in a while)

mirage island that has leichi berries to collect.

it's a plateau  with some patches of grass and the leichi berry plant gives 1 leichi berry per # of hours or something

navel rock from the ho-oh  and lugia event back in firered and leafgreen

sharp steep rock with at the base an easy tunnel going straight downwards by jumping on rocks to an underwater waterfall. the rocks may or may not break leading you to fall but be vunerable to lugia's first and strongest attack (if lugia is made into a boss)

Another tunnel at the base that goes up but with stones that get hotter and hotter dealing damage to non-fire types, but fire types would have difficulty scaling to the peak due to water dripping from the stalactites that would do damage to the fire types(doesn't heal water types) speed and precision is needed to get to the top to the exit where ho-oh roosts. 

mike hates co-existence confirmed

Hall of Origin where arceus was

Birth Island of Doxys

The Sky Pillar of Rayquaza

Cloud Tower of Rayquaza (mystery dungeon blue)