Well, the games that can be played on the 3DS that are Pokemon main games are Pokemon Diamond, Pearl, Platinum, Heartgold, Soulsilver, Black, White, Black 2, White 2, X, Y, Omega Ruby, and Alpha Sapphire. Personally I've played each and every one of those, but if you're just getting into Pokemon you might want to save on money too. It's hard for me to decide on just one of those to play; they're all great games. But if you get the chance over time make sure to try one from each generation:
Gen4: Diamond, Pearl, Platinum
Gen1and2: Heartgold, Soulsilver
Gen5: Black, White, Black 2, White 2
Gen6: X/Y
Gen3:Omega Ruby/Alpha Sapphire
Btw those are listed as the generations of the regions they represented. Chronological order of when they were released was in my first paragraph.
Also, I started the Pokemon Anime and Games with Diamond, and moved on from there, still being able to experience the first 3 generations' regions thanks to HG/SS/OR/AS.
Finally, once you've got a taste for some of the main games in Pokemon, in the future if you're ever looking for more Pokemon, Pokemon has a wide and expansive list of Spinoff games for the Wii, Wii U, DS, and 3DS (all DS games can be played on the 3DS). I personally recommend trying Pokemon Mystery Dungeon, one of the first ones (NOT Gates to Infinity) like Pokemon Mystery Dungeon Explores of Time, Darkness, or Sky.
There's literally so much to Pokemon nowadays including the Anime, Manga, main games and spinoff games that it can't be experienced quickly. After playing X/Y or OR/AS, try out some of the other games too whenever you have the spare money to spend. Trust me, you won't regret it.
