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My Top 3 favorite core series Pokémon games list honestly has a lot of close calls, but in the end, I've settled down with the following list:
3. FR/LG
The original Kanto remakes. LeafGreen was the very first Pokémon game I ever played in 2013, which also contributes to these games' position on my list. However, the main reason is that if you want to experience the "original" adventure through Kanto, these games offer a way better version of that experience than the admittedly outdated and glitchy Generation I games, and are perfectly serviceable even by today's standards (even if I'm still looking forward to how the Let's Go! games are going to improve on the Kanto region even further). Plus, we also have the Sevii Islands to expand Generation I's non-existent post-game and provide us with some backstory to the events of Generation II and Team Rocket's return.
2. B2/W2
The sequels to Black and White. I honestly feel kinda bad leaving the original two games off the list, but the sequels quote honestly outshine the original ones in my eyes. The Pokédex has been expanded, new areas have been added, old areas have changed, many characters from the first games return with new roles and looks, tons of side stuff to do even after beating the game... These games are just brimming with content! Pokéstar Studios! Join Avenue! Pokémon World Tournament! Black Tower and White Treehollow! The list goes on! And the post-game, where you get to, among other things, explore the early-game areas from the previous games and even visit your old hometown from Black and White... One of the best post-games of all time in Pokémon!
Honorable mentions (not in any specific order):
Emerald - An awesome game, which still holds up there amongst the best representations of Hoenn, even with OR/AS, which honestly deserve an honorable mention too. I love how you actually fight both evil teams in this game, and Team Magma has a way more fitting base. Also, the Battle Frontier.
Platinum - Easily the best Sinnoh game to date. Improved story and mechanics, Looker, the Distortion World, an improved post-game story, and the Battle Frontier. Also carrying onward from the original Diamond and Pearl, the Battle Zone as a whole. An entire sub-region of Sinnoh reserved just for the post-game, with its own routes and "towns".
X/Y - The transition to 3D improved the outlook of the games significantly, and the Kalos region's design takes full advantage of this, with stunningly beautiful locations. The music is great too, and I feel that the characters and story of these games are seriously underrated. It's honestly a shame we didn't get Z, because, as many have said, the region feels a bit incomplete. Zygarde would've deserved its own game instead of having its special gimmick being hastily shoved into the next generation.
US/UM - I personally enjoy these games more than the original S/M. While I admit that there are some details that could have been changed to significantly improve the quality of the product (like having the Ultra Recon Squad do more than just provide exposition for most of the time), it's still good enough for me. I personally liked the changes made to Lillie, Lusamine, and Hau's characters, and the new locations and features added to these games expand the region nicely. Also, Team Rainbow Rocket. Love it. One of the best post-games stories ever, if not the best.
And now, to the actual number 1...
1. HG/SS
These games may not be quite as advanced as the Generation V games, but they still have a ton of content. First of all, they take everything from the original Generation II and bring it up to date with improved graphics and mechanics. The Johto region looks absolutely beautiful on Nintendo DS, and the characters have been improved as well, like the rival getting more backstory and the Team Rocket Executives getting actual names. And of course, the post-game. This post-game is an outright legend among Pokémon post-games. Sure Johto may have borrowed a lot from Kanto, but it all pays off big time when you get to explore an entire second region for the post-game, with another set of eight Gyms to challenge and multiple changed locations and characters to see. At it all ends with a battle against the previous player character, who uses Pokémon of ridiculously high levels. Nothing short of iconic.
Secondly, these games are improved even further with the new things that were added to them compared to the original games. The walking Pokémon feature, the Pokéathlon, the Johto Safari Zone, many of the shrunken/removed Kanto locations being restored to their former glory, the Kanto Legendaries being available to catch, the Hoenn and Sinnoh sounds, the Gym Leader and Pokémon League rematches, the Battle Frontier... Heck, even Suicune's story was extended to reach the post-game this time around!
So, to put it shortly, these games are my favorite core series Pokémon games (and Pokémon games overall) because they take something that was already great, update it with the newest mechanics while staying true to the original source material, and then seamlessly add in some new material to expand the experience even further. Quite honestly, the only outright bad thing I can say about these games is that TMs are not reusable. That's it.
3. FR/LG
The original Kanto remakes. LeafGreen was the very first Pokémon game I ever played in 2013, which also contributes to these games' position on my list. However, the main reason is that if you want to experience the "original" adventure through Kanto, these games offer a way better version of that experience than the admittedly outdated and glitchy Generation I games, and are perfectly serviceable even by today's standards (even if I'm still looking forward to how the Let's Go! games are going to improve on the Kanto region even further). Plus, we also have the Sevii Islands to expand Generation I's non-existent post-game and provide us with some backstory to the events of Generation II and Team Rocket's return.
2. B2/W2
The sequels to Black and White. I honestly feel kinda bad leaving the original two games off the list, but the sequels quote honestly outshine the original ones in my eyes. The Pokédex has been expanded, new areas have been added, old areas have changed, many characters from the first games return with new roles and looks, tons of side stuff to do even after beating the game... These games are just brimming with content! Pokéstar Studios! Join Avenue! Pokémon World Tournament! Black Tower and White Treehollow! The list goes on! And the post-game, where you get to, among other things, explore the early-game areas from the previous games and even visit your old hometown from Black and White... One of the best post-games of all time in Pokémon!
Honorable mentions (not in any specific order):
Emerald - An awesome game, which still holds up there amongst the best representations of Hoenn, even with OR/AS, which honestly deserve an honorable mention too. I love how you actually fight both evil teams in this game, and Team Magma has a way more fitting base. Also, the Battle Frontier.
Platinum - Easily the best Sinnoh game to date. Improved story and mechanics, Looker, the Distortion World, an improved post-game story, and the Battle Frontier. Also carrying onward from the original Diamond and Pearl, the Battle Zone as a whole. An entire sub-region of Sinnoh reserved just for the post-game, with its own routes and "towns".
X/Y - The transition to 3D improved the outlook of the games significantly, and the Kalos region's design takes full advantage of this, with stunningly beautiful locations. The music is great too, and I feel that the characters and story of these games are seriously underrated. It's honestly a shame we didn't get Z, because, as many have said, the region feels a bit incomplete. Zygarde would've deserved its own game instead of having its special gimmick being hastily shoved into the next generation.
US/UM - I personally enjoy these games more than the original S/M. While I admit that there are some details that could have been changed to significantly improve the quality of the product (like having the Ultra Recon Squad do more than just provide exposition for most of the time), it's still good enough for me. I personally liked the changes made to Lillie, Lusamine, and Hau's characters, and the new locations and features added to these games expand the region nicely. Also, Team Rainbow Rocket. Love it. One of the best post-games stories ever, if not the best.
And now, to the actual number 1...
1. HG/SS
These games may not be quite as advanced as the Generation V games, but they still have a ton of content. First of all, they take everything from the original Generation II and bring it up to date with improved graphics and mechanics. The Johto region looks absolutely beautiful on Nintendo DS, and the characters have been improved as well, like the rival getting more backstory and the Team Rocket Executives getting actual names. And of course, the post-game. This post-game is an outright legend among Pokémon post-games. Sure Johto may have borrowed a lot from Kanto, but it all pays off big time when you get to explore an entire second region for the post-game, with another set of eight Gyms to challenge and multiple changed locations and characters to see. At it all ends with a battle against the previous player character, who uses Pokémon of ridiculously high levels. Nothing short of iconic.
Secondly, these games are improved even further with the new things that were added to them compared to the original games. The walking Pokémon feature, the Pokéathlon, the Johto Safari Zone, many of the shrunken/removed Kanto locations being restored to their former glory, the Kanto Legendaries being available to catch, the Hoenn and Sinnoh sounds, the Gym Leader and Pokémon League rematches, the Battle Frontier... Heck, even Suicune's story was extended to reach the post-game this time around!
So, to put it shortly, these games are my favorite core series Pokémon games (and Pokémon games overall) because they take something that was already great, update it with the newest mechanics while staying true to the original source material, and then seamlessly add in some new material to expand the experience even further. Quite honestly, the only outright bad thing I can say about these games is that TMs are not reusable. That's it.