As far as the Pokémon in said Generations go, I like the 1st one and the 3rd one the most. Both had mostly new Pokémon, and all had quite nice designs overall. Many 1st gen ones were quite plain, I reckon, but there were quite a few with cool designs. The 3rd Gen blew me away with such awesome Pokémon that ranged from quite weird animals to even artifacts of sorts. And well... I liked the fact that I was introduced to them properly. I happened to know them well, and that's why I'm most attached to them...
In terms of Regions... I like them all. However, I lean mostly to Orre (Poor neglected place...
), Hoenn and Johto. I like the setting of Orre too much, for it's not the usual happy-go-lucky place and is under the control of evildoers that harm Pokémon in the worst way imagniable. Might not be much variated in terms of natural places or cities, but I love the background a lot. Hoenn is awesome for the cool environments it has. Desert, volcano, islands, forest, mountain... the list goes on. It's not always forest and green areas every other Route. I also like the Cities. They're all creative and interesting, despite the slight lack of background. I also like the characters and the Pokémon it has a lot. Johto was great too. It had a quite nice background and culture added on to it, not to mention the absolutely best GYM Leaders of all time (As far as character and personality goes.). But it was ruined by having no identity whatsoever and being just a Kanto subordinated, as ~*CB*~ and Eszett said. Not to mention the utter lack of 2nd Gen Pokémon in it, and the outrageously wrong abundance of Kanto Pokémon. 2nd Gen Pokémon can't be called Johto Pokémon in any way, seeing how a big bunch of them wasn't available in said Region... hadn't that be the case, it could've been my absolutely favorite Region... =/
And in Games terms... the 3rd Generation. 'Nuff said...