Not too famiar with the games anymore theses days. And haven't played one since the original gameboy color. So not sure what the compatability with the games are anymore on the 3ds. Would be fun to go back through and play yellow, etc..
The 4th Gen. Pokemon Diamond/Pearl/Platinum take place in Sinnoh. Platinum is the third (and best version of the games). Pokemon Heart Gold / Soul Silver are remakes of Gold and Silver, sequels to RBY.
The 5th Gen
Pokemon Black / White take place in Unova and use only new Pokemon until the Elite Four. Pokemon Black 2 / White 2 are sequels to BW that make Unova more diverse and better to play.
Also Trozei, Conquest, Mystery Dungeons Explorers of Time, Space, and Sky, all Pokémon Rangers, Mystery Dungeon Blue (much older now), Rumble Blast, Dash (super old), and the upcoming Pokémon Mystery Dungeon Gates to Infinity.
Those are sidegames, and of them I most recommend Explorers of Sky and Conquest.