Based on actual gen pokemon, geography and story
1) Hoenn - Awesome pokemon and storyline, also really liked the diversity of the region with volcanoes, deserts and ingame weather. music wasn't great but it hasnt had DS appearance yet so cant be slated too much.
2) Kanto- Originals are hard to beat and I only place it below Hoenn due to a lack of diversity and a lack of post game content but still a classic and the original 151 will always be the best set.
3) Johto, HG/SS IMO is the best set of games so far, gold and silver were so enjoyable and with Kanto also in the game its just brilliant, Johto had an interesting map and great game plot and I always found it enjoyable, also theres always something fun to do on HG/SS the only thing that lets it down is that the pokemon release din this region weren't as good as 1st or 3rd. ANNNND It had the S.S. Aqua music, which is just the best game music ever
4) Unova, Black and white are revolutionary games to the series and the whole plot of the games and actual gameplay was on a new level, but I hate the geography and over half the new gen pokemon just look rubbish, the legendaries look more like mechs than creatures and some designs just lacked imagination, also the whole circular region with no middle bit hacked me off.
5) Sinnoh, Liked most of the pokemon but the story was boring, Team Plasma's plan was just a bit meh and lacked any interest personally and I hate the map they gave us. Still an enjoyable game due to it being a member of the pokemon franchise, alos the legendaries were verging towards mechs at this point