Each game had it's ups and downs for me, but each one also holds a specific stage in my growth as a player.
Kanto: 100% Nostalgia. being like 8 or 9 the first time I played, it was simple to understand, had a small story to keep me entertained, and with each play through, I seemed to find something new. Yes running back and forth got old, but I didn't mind that, seeing as I'd normally miss something the first time through.
Jhoto: the region in it's self was a bit off for me (my least favorite layout when it comes to over-world) but by the time I got Gold and Silver, I understood a bit more. the random encounters of the legendary Dogs (i prefer gerbils lol) always came as a shock, and the multiple side quests made back tracking more interesting, such as the Unown Puzzles, The Lapras event, and the Huge expanse that was Mt. Mortar. It only needed one more thing to make it perfect for me, more Dark and steel type pokemon.
Hoenn: This was by far my favorite, the region was by far the coolest layout, i loved the Dive HM, and the colors! after seeing only a hand full of colors in the games to rainbow explosion made the game stand out like no other at the time. The downfall how ever was simple; the legendary Pokemon, there were just too many. the other turn off for me was no Team Rocket, after several years with the misfit bunch, I was sad to see a 100% lack of them (Besides Aqua and Magma annoyed me their ideals were totally lame).
Sinnoh: My least favorite, by this time, I was expecting a mega challenge, huge routes, horrifyingly long caves, and a bad guy team to redeem Pokemon's water and fire fiasco. But alas, the routes were so-so, the side quests were mainly for items i don't use, the layout was awkward, and the chance of either a fire starter or ponyta left me extremely upset. but there were some decent points, the snow routes were interesting, the graphics were different, and there was the undergound (which i spent way too much time in).