maybe cruiseliners(ie ss anne/aqua) that goes around the regions in a circle daily?
mon: slateport(lilycove?)-olivine
tues: olivine-viridian
wed: viridian-sunnyshore?(veilstone? snowpoint?)
thur: sinnoh-viridian
fri: viridian-olivine
sat: olivine-slateport
and maybe also the magnate train from rustboro-goldenrod-saffrom-jubilife
for the orange islands there would be a ferry to the main orange island(moi) from viridian/olivine(either as another stop on the circuit or a separate ferry) and then another ferry would take you to and from any orange/sevii island
another ferry should also be in hoenn to go from slateport to lilycove and any other island
Having it be day based would be too much of a pain. Easier to have em accessible any day but after certain customized conditions are meant say earn at least 3 Badges from a connecting reason as for boats make it easier and have them set up as such ( aside from existing boats in each respective region & Version ):
Boat#1 - SS Aqua II runs between Pallet Town ( Extend the pier in the example quoted below ) , One of the Sevii Islands, One of the Orange Islands and an extended Pier in SlatePort City for Hoen ( Ruby/Emerald/Sapphire era ). These would ALL be accessible from Pallet.
Boat #2 - Sevii Ferry . Similar to in FR/LG this ferry would run to Islands that can't be reached merely by surfing
Boat #3 - SS Snow ( Name just an Idea ) Create a Pier next to the Global Terminal ( If GT is added) Or replace the GT With a Pier. This ship would run from Goldenrod Pier to SnowPoint City in Sinnoh
Boat #4 - SS Explorer ( Again just a random suggestion ) Would also Run from Goldenrod Pier to either an unused or newly added pier in Casteila City
Boat# 5 - Oran Ferry - Would run between various Orange Islands not reachable by surfing ( Sorry Lapras & Lapras Fans

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The rest are just suggestions if incorporating even more regions:
SS Orre - Create a Pier in Driftveil then run it to Gateon Port
SS Almia - Would Also Run from Driftveil Pier but to Haruba Village
SS Oblivia - Would Run from Unity Pier to where in Oblivia
SS XY - Also from Unity Pier to wherever fitting once X and Y versions are further revealed
The orange league ferry if I remember rightly, actually leaves from Pallet Town according to the anime, and since there is a southern coast of Pallet Town, it wouldn't be that hard to extend a pier out and have the ship dock in there. maybe add a small building or a ticket booth.
The only problem I see with having the ranger regions, and some of the islands in the Orange League, is that they don't necessarily agree with catching Pokémon in balls in some places. One of the orange islands actually outlawed it because it's a nature sanctuary. Maybe it could be an island/s with no random encounters... But perhaps you could run into either Team Rocket or the Pinchers trying to steal Pokémon and you're enlisted by some rangers to help out.
Agreed but some of the areas that "don't agree with catching Pokemon" could I'm sure be modified easily enough though I do like the side quest-esque ideas of running into Team Rocket or some other evil team or the helping rangers idea. I also wouldn't mind seeing some cities from the Anime that never got any in game loving be added to a game