They COULD have adjusted the lore to explain this, but no, non-Alola Dex Pokemon don't get Dex entries. Not even through Pokemon Bank's update. Maybe if we get gen 4 remakes they'll explain it... if Arceus gets the Deoxys treatment and we're finally allowed to enter the Hall of Origin. Not holding my breath, however.
I don't think they'll ever make Arceus a plain Legendary, if anything I'd imagine Darkrai would be the next Mystical to get demoted to Legendary (who I think has a ton more story potential than Arceus does, at least in ways you can go and portray Darkrai). Maybe they can extend the way we got Cresselia in the original games to fully include Darkrai in it which results us in eventually capturing both.
Manaphy could be another option, Gen IV had two Cute Mystical Pokemon and Manaphy's original method of distribution was special: it was obtained via completing the Pokemon Ranger games. Unless they release another Pokemon Ranger game (which I wouldn't mind, the Switch's screen is a touch screen (though the game will need to be packaged with a stylus (and some screen protectors wouldn't hurt either to throw in))) or something similar it'll either be distributed like any other Mystical Pokemon OR they could just demote it to Legendary and make a story around it post game (Pokemon Rangers are a trainer class in the games, though Sinnoh Rangers seem to be normal trainers compared to the ones in the Ranger Games that uses the Styler to befriend Pokemon without needing to catch them).