Since the first game they rereleased was FRLG, I find it hard to belive that they'd go back to the GB versions. Next rerelease they'll go for will probably be HGSS, which'd be interesting because I don't think there have been any DS games ported to the Switch, not ones published by Nintendo at least.
I do wonder what they'll do when they rerelease RSE since ORAS is pretty diffrent and RSE is, from what I'm aware, considered the more iconic version. Personally, I just wish they're release both the originals and the remakes.
