My favorite generation of Pok?mon depends on the exact classification of generation.
In terms of regions, my favorite is a toss-up between Unova and Johto. I greatly enjoy traversing both of these regions and am fond of pretty much everything about them. The Pok?mon are great, the characters and stories are enjoyable enough, and the locations themselves are good. Upon consideration, nostalgia wins out for me because for as good as Unova is in all regards, Silver and Lance were great cool, the starters are some of my favorites, the gym leaders are pretty good, I love Ho-Oh and the legendary beasts, and apricorn balls were a fun mechanic. Oh, and the Pok?athlon Dome added in HeartGold and SoulSilver was a fun way to spend some time.
In terms of Pok?mon introduced in a generation, it kind of has to be the original 151 from Kanto for me. 2nd and 3rd place would probably be Unova and Johto, in that order.
In terms of overall enjoyability, I somewhat hesitantly feel that I have to give it to Generation 6. While Kalos is easy and disappointing with no Elite 4 level scaling or anything, it introduced trainer customization and a few of my personal favorite Pok?mon, like Gourgeist and Malamar. Meanwhile, while the Hoenn remakes didn't include trainer customization, they offered more challenge than was present in Kalos and an enjoyable way for me to traverse Hoenn since I had quit Pok?mon in the years spanning from after Crystal's release up to the release of HeartGold and SoulSilver due to peer pressure and only got back in because a friend told me about HGSS and it invoked nostalgia. The absolute biggest things in Generation 6's favor, though, are the changes made to breeding and EV training. The Destiny Knot being used to pass down IVs from parent was amazing, and it was nice to be able to pass down the Pok?ball of the mother to the offspring. Super Training, meanwhile, made EV training simple to keep track of and made it go by relatively quickly compared to hunting down specific Pok?mon to knock out in the wild. People say the EV training methods in Generation 7 aren't bad, but for me it was an enormous step backward to remove Super Training. That's a feature that ought to have been present in every game from then onward.
TL;DR:
Region - Johto narrowly beats Unova
Pok?mon - Kanto, then Unova, then Johto
Overall Games - Generation 6