I think R/B/Y and Crystal were all re released for the 3ds in the past year if you want to nostalgia out.
And the 3ds native Pokémon games are X and Y (New stuff), Omega Ruby and Alpha Sapphire (Ruby and Sapphire remakes), Sun and Moon (new stuff), and Ultra Sun and Ultra Moon (more different'er new stuff).
I don't think anyone actually cares about the 3d stuff the 3ds can do so the best hand held now is probably the New 2ds XL (A 3ds with 3d disabled).
The DS games Diamond, Pearl and Platinum, Black and White, and Black 2 and White 2, Heart Gold and Soul Silver. Also exist, and are probably better games than all the 3ds ones, and the cartridges are all playable on 3ds.
But online services for all of them is suspended now I think (besides Pokébank, I guess).
Personally, I don't think I've actually enjoyed a game since Emerald, So I'm probably not the person to ask which of the new ones is best.
This post was edited by Mcn00bin on Feb 28 2018 09:35pm