[b]Ok, I worked out how every area connects after some thinking. Some areas will probably be added later, such as caves and other towns.[/b]

Starting at Sharpedo Bluff, Treasure Town to Secluded Beach through Beach Cave to Shallow Beach to Miracle Sea to Tree Top Safari to Midnight Forest passed Earthquake Mountain to Hidden Jungle to Bottomless Sea, then passed Sky High Mountain to Foggy Forest, to Fogbound Lake, to Bountiful Sea, to Furnace Desert, to Infernal Path to Scorched Plains passed Blazing Inferno (Volcano) to Post Town to Pokemon Paradise to Everlasting Woods passed Moonlight Mountain to Moonlit Valley to Moonlit Village to Serene Sea through Cryptic Cave to Wild Plains to Blossoming Flowers to Shaymin Village passed Sky Peak Mountain to Blooming Paradise to Waterfall Lake to Eternal Forest to Deepwater Swamp to Mystic Woods to Dust Forest to Scorched Desert to Sandpit Desert to Rainbow Valley to Rainbow Peak to Star Cave to Starlight Plains to Sunset Peak Mountain to Icicle Field to Frozen Lake passed Frozen Top Mountain to Blizzard Island to Frozen Forrest passed through Crevice Cave to Storm Mountain to Flyaway Forest to Mystic Crater through Crater Cave to Devil's Sea through Seafloor Cave to Sacred Field through Aegis Cave to Concealed Ruins through Echo Cave to Miracle Sea to Shallow Beach 

Nothing connects passed here.

Great Glacier to Glacier Palace to Glove of Whispers

Special Rift 

Shadowrealm Valley to Nightmarish Cave  

Miracle Sea to Hidden Land to Temporal Tower End:

Skycloud Tower