Generation 6 makes a strong case for me, despite some downsides, and it's the one I've most consistently said has been my favorite over the years.
The quality of life improvements to breeding that made it simpler, faster and less of a hassle (Destiny Knot passing on at least 5 IVs, Everstone 100% passing on the Nature of the holder) are greatly appreciated, as is the fact that X & Y started the trend of Move Relearners being able to reteach egg moves you might've bred onto a Pokémon but had replaced whether intentionally or accidentally. I really love the Super Training as a method of EV training and found it easier and more convenient to keep track of as opposed to having to battle Pokémon individually. The Player Search System was more preferable than what has come afterward. The abandonment of Mega Evolution is a tragedy, it's the best gimmick they've had for a while. It also introduced trainer customization, which is great, though it's a shame that they didn't have it in ORAS. Finally, a relatively minor thing, I wish we'd get the option to have some other characters call us by a nickname like they had in X & Y (even if the defaults were god awful and I came up with my own).
I prefer Generation 6 over 7, which retains a number of things, because of the traditional gym format and because of the PSS and Super Training. Generation 7 is still great and I love it nearly as much, just personal preference. I will say that X & Y is dragged down by the fact that the Elite 4 doesn't raise their levels upon rematch, so ORAS does a lot of the heavy lifting. I've seen some people criticize ORAS for being different from original Ruby/Sapphire/Emerald, but I had initially skipped the original Gen III (stopped playing after Crystal, returned with HGSS) so ORAS was my introduction to the Hoenn region and I really like it. I've since played the original Gen III, and it does suck that the Battle Frontier is missing, but it is what it is.
--
Generation 7 is probably second because I'm a creature of convenience and I like the gradual improvements made to the series with each game, so Generation 7 enjoys a lot of quality of life features from past games all rolled into one, plus it has the most Pokémon we have ever and will ever be able to choose from since the National Pokédex and Pokémon Bank allowed you to transfer in any Pokémon you wanted. Original Sun & Moon has the better story, while Ultra Sun & Ultra Moon have the more engaging gameplay and features.
Finally, I'll give Generation 5 the third place spot. They're the final installments with sprites, which were delightfully animated. The Unova region is fun, the plot is probably the best, the music is great. The Pokémon World Tournament in Black 2 & White 2 is also a really neat feature. I really enjoy the Unova region's selection of Pokémon (I even like Trubbish and Garbodor and don't hate the Vanillish line) and I was totally open to just having entirely new Pokémon in the initial playthrough. I feel like people really missed out on great games if they skipped out on Generation 5.