I'm still deciding between Generation 5 and 6 - I'd put them both equally 1st.
Majority of my favorite Pokemon got introduced in Generation 5 (such as Watchog, Mienshao, Mienfoo, Patrat, Minccino, Cinccino, Purrloin, Liepard, Emolga).
My favorite Pokemon features are on Generation 6 - especially Amie.