1) G/S - THE nostalgia game for me, I couldn't not put this as number one. Amazing game too. This is the game all my good memories are attached to. The region is great, soundtrack even better.
2) HG/SS - Should really be number one, it made G/S so much better. All the good things we'd gotten from RSE and DPPt were crammed in along with the Pokewalker, it was like nostalgia on steroids that still stands today as being one of the best Pokemon games of all time.
3) RBY - My first Pokemon games, up here because of significance really. I find the mechanics are harder to go back to than even G/S. Kanto wasn't my favorite region, but even out of historic context the first 151 Pokemon are fantastic.
4) DPPt - I loved Gen IV, this felt like such a huge comeback compared to RSE which I never liked much. So many legendaries, amazing region, great new Pokemon. I feel the anime had rejuvenated sometime around here too and Wi-Fi was just the icing on the cake. Pokemon on the DS felt like such a jump.
5) X/Y - Fantastic region, felt like light at the end of the tunnel compared to the darkness of BW/BW2. The new Pokemon were great and so many features make the game insanely playable even today.
6) OR/AS - Maybe a tentative entry as I'm still only at Fortree right now. Very enjoyable, the region has been made much more interesting than I found the original Hoenn. Pokenav is great, loads of features.
7) BW2 - Improved greatly on B/W and felt much more like Pokemon should. Still had some of the dark, more industrious elements of BW Unova but opened up so much more of the map. Could have been incredible if it wasn't living in BWs shadow.
FRLG - Even when this was freshly released I didn't have much interest in going back to Kanto. Did a good job bringing everything to colour in the GBA style and added some interesting new features/locations but overall I was fairly apathetic.
9) RSE - Never liked Hoenn much and I don't know why. I felt like R/S came from a very different angle to G/S/C/R/B/Y and I had trouble believing it was the Pokemon world, it felt more like a fan game. Still introduced loads of great things into the gameplay.
10) BW - Maximum effort on the story but I didn't like it much anyway. Felt far too much like it was chasing the nighttime anime trend in Japan at the time by following typical anime cliches. The region was so dark and depressing in comparison to HG/SS and all the Pokemon seemed to feel like bad knock-offs of Gen I Pokemon. In retrospect, it's more interesting but at the time I wondered if Pokemon was finished.