Here is how I would rank them: 2/3/6/5/4/1*
I gotta give it to gen2 for the "best" generation. It just had more content than any other games in the pokemon series. there were 16 badges with 300+ pokemon to collect in the game. You could even re-battle trainers daily if you wanted to. There were just more things you could do in the game everyday than in other series. At the time the games also felt like a big leap forward for the franchise, introducing 2 new types, new poke balls, planting things, ect. With a game like pokemon, where you only have 1 save and you are not likely to start over again, so contant means everything to me. I don't even have my Crystal version anymore (unlike all the other gens, where I still have at least one game) and yet I remimber it being my favorite even to this day.
On a personal level, gen3 was my favorite. I like the variety in the environments, the weather system, the fact that it looked prettier compared to the Gameboy Color generations, the contests (seriously),the PokeBlock mini game (seriously), and the secret bases (I wonder if anyone else even remimbers that feature). Also, it had some of my favorite Pokemon in terms of design, becuase most of the new pokemon seemed to draw their inspiration from real animals which I dug.
Gen6, is the most polished game and by far the prettiest in the series. I love Pokemon-Amie (yup, I'm serious), Super training, and pretty much all of the new features introduced in the game. Especially the online system, which is robust and easy to use. The music was really a stand out, and I like all of the few new pokemon the game introduced. But I felt it was really undone by its weak story, well, mainly just Team Flare who was by far the most forgettable bad-guy team to date. In addition is there is very little after game content to look forward to (DLC might fix this however). This would be my second choice for best if I wasn't so nostalgic for gen3.
Gen5 had the best story hands down, but I don't think that's really saying much for this series to be completely honest. There wasn't much else in the game that stood out. Expect the animated sprites, which looked cool at first, but I felt was an ugly design choice overall, given how blocky and muddy the pokemon would look from time to time.
Gen4's introduction to the global link system did very little to impress me as a non-compentive player. This generation's new Pokemon designs were my least favorite becuase of how in-organic looking most of them were. But most importantly noting really stood out to me as a player in this generation, except maybe the Underground (does anyne remimber that?). Which I thought was a nice distraction at the time. I liked the Poffin mini game, but I did not like the Super Contests as much as the beauty contests of the pervious gen.
Gen1 has not aged well at all, it's incredibly clunky at times and it looks pretty ugly to boot.
*That little essay should have given a hint at what type of player I am. I don't care much about the meta game or competitive battling. I'm mostly superficial and prefer a good single player experience overall.