Quoted By:
Johto
Pros: lots of exploration and optional worldbuilding, two regions to interact with
Cons: Team Rocket's pacing is a big clusterfuck on an otherwise enjoyable experience
Unova
Pros: story structured like other JRPGs including the character interactions, enjoys imparting life lessons to the player
Cons: plays it safe with the messaging, BW2 goes back to more traditional Pokemon storytelling (still has pros however)
(Sun and Moon) Alola
Pros: characters first and foremost in the story, but doesn't completely ignore Pokemon either
Cons: intense railroading, no cutscene skip on repeat playthroughs
Pros: Pokemon and human characters simultaneously important and developed during the story, no railroading of any kind
Cons: SV is buggy as fuck, Area Zero's first visit is incredibly padded out
Honorable Mentions
(Platinum) Sinnoh: More standard Pokemon story but was the beginning of GF trying more things with character interactions
Hisui: Simple-ish story that focuses on characters (but mainly Volo) that can get bogged down by graphics and the gameplay loop, very different to the rest of the series
(Ultra Sun and Ultra Moon) Alola: Everything I said for Alola but new side characters added. Ironically has a worse story than the originals but has better gameplay tied to it
I'm very biased though. Picrel.