Excluding remakes and sister games:
1. Pokémon Gold / Silver
2. Pokémon X / Y
3. Pokémon Ruby / Sapphire
4. Pokémon Diamond / Pearl
5. Pokémon Red / Blue
6. Pokémon Black / White
If this was a month ago, I'd probably put RBY higher, but after playing through Yellow, I realized how frustrating Gen 1 is. For some reason things like missing, Confusion, Poison, etc. seem much more common. I also hate how the bag is so unorganized and how fast you run out of room for items (including the PC even).
Black and White make the bottom for me since I really had no interest whatsoever in Unova, I hated the zoomed-in pixel-esque graphics when battling, and the story felt so long and tedious for whatever reason.
Diamond and Pearl are okay I suppose, but the gameplay feels so~~ slowly paced. Sinnoh is a meh region for me, not bad but not great. For me, most of the Gym Leaders / Elite 4 members have nothing special about them and nothing to remember them by. Except for Crasher Wake.
I enjoy Ruby and Sapphire, but their Gym Leaders and Victory Road are the most frustrating. I also dislike the cut off from a LOT of Kanto / Johto Pokémon.
X and Y took time to get used to, but I find them great now. The story doesn't feel as though it drags on forever, the graphics look great, I like the character customization (which I find stupid they didn't keep in ORAS), and I like how convenient breeding for competitive Pokémon is compared to older gens. On a side note I was also glad Mewtwo was added in the post-game.
Gold, Silver, and Crystal remain my favorite games for some reason I can't really explain. For whatever reason I could play through the game(s) so many times without getting tired of them. I really like the fact that there's two regions to travel to and 16 badges to obtain. I mean seriously, why hasn't this idea continued?