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My Recommendations:

First, don't worry too much about playing the games in order. Pokemon games are only slightly more closely connected than Final Fantasy games, with each game providing all necessary info for newcomers.

 

Recommended

  • Red/Blue - The earliest games in the series, but they've held up pretty well. The gameplay is a bit unbalanced or archaic at points, but not nearly to the extent of, say, NES RPG's. This version also uses the same group of Pokemon as Pokemon Go, and is also on the 3DS Virtual Console.
  • FireRed/LeafGreen - Vastly improved remakes of Red/Blue, not just in graphics but also in interface, gameplay. I'd recommend this one over Red/Blue except that it is less convenient to find and play nowadays, since Red/Blue sold so well and had a Virtual Console release.
  • HeartGold/SoulSilver - The remakes of the Game Boy Color games. a lot of people love this generation, and it has to be commended for its interesting environment and loads of content. That said, it has become one of the most expensive games in the series, costing more now than it did at launch.
  • 3DS entries - Solidly made games that are very user friendly. I'd recommend them to most RPG players with a 3DS. XY and the Gen 3 remakes each have their pros and cons, but a lot of that is based on taste.

 

Discouraged

  • Yellow - Though mostly the same as Red/Blue, Yellow had a few changes to appease fans of the anime. For newcomers though, the changes mostly make the game unnecessarily harder and have less varied random encounters.
  • Diamond/Pearl - Though not terrible games, they start off slowly and have somewhat cumbersome environments to traverse. Platinum is better, but is too hard for beginners.
  • Black/White - Not newbie unfriendly, and honestly rather good, but these are best experienced after playing other games in the series. Its distinct rosters of species and storyline are a bit out there for this series.