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I'll say that Hoenn are my favourite games and i half anf half agree with you.
>can't visit older regions after beating the Champion
Yes, it was cool in GSC, but it was also a direct sequel and before HGSS Kanto was basically nothing but a boss rush. All the dungeons were stripped down, no legendaries, you basically just go through to get a handful of new Pokémon that aren't even particularly good and fight Red.
>can't rebattle the protagonist
Again, wouldn't really work due to it not being a direct sequel. It's set at rhe same time the Kanto games take place anyway.
>no day/night cycle
Yeah this one is legitimately shit and it's sad the only way to view Hoenn at night is the awful remakes. At least the functionality is there for things that need it.
>no radio/phone calls
Radio was cool, the phone calls were kind of cool, but honestly they weren't much more than flavour dialogue shoved in your face every 5 minutes. Emerald brought phone calls back anyway.
>can't transfer your old Pokemon to the new game
I moved this to last because I do think this is actually worth discussing in detail. In my opinion the removal of the Time Capsule was the biggest mistake made in the series and if it had been included it's very likely the nostalgia cycle wouldn't be as heavily focused on. FRLG were made pretty much just to bring back Kanto + Johto Pokémon. What would the games look like if you were expected to transfer them over instead? We probably never would've seen remakes until around 2010ish, and it could be that they would be more grand affairs. What if they ended up as proper reimagining on consoles instead? Not likely, but still. I also think Dexit might not've happened. It would only mean a few extra years people were carrying things up all the way to swooshie, but having that uninterrupted line of bringing your bros all the way up would probably piss people off a LOT more if they couldn't have a 2 decade old Pidgeot or whatever chilling in Galar. RS set that precedent