For me, my favorite Gen would be V. Why? I finally, after so many years, got me a pair of "I will love you forever" faves: Golett and Golurk. I admit it--I was on the fence when it came to Gen V until I spotted the sprite of what looked to be a giant robot...
Of course, Gen V having a great story and adding the Musicals--yes, I like them!--also helped.
I think my least favorite would have to be II. I've found that a good number of the Johto Pokemon just aren't all that memorable and the story was a bit lacking. Johto did have good music however, so I'll give it that. (Not saying I didn't enjoy the games; they just felt a little lacking in my book.)
I... I... Yes, this, excluding the Golett/Lurk part, and even a bit, cause I still adore the family, Gen V brought me so many of my favorites, I never even had any favorites before it, the region, the plot, the characters, music, musicals (for I also like them, they're cute).
Gen III to me is also on a high spot for its great diversity and a gameplay that just... flows really well, and I also liked the enviromental messages, which is rare since I usually hate those.
Gen II was just... weak, IMO, it felt like it was just clinging so hard to Gen I that it never found its own purpose, which is a shame, since I think Johto, as a concept, could be worth a lot more, perhaps, in a future game, when Kanto is inacessible, Johto may receive its own glory in the name of better execution.