Well, Gen V had Meloetta and that instantly makes it my favorite, but other than that, I think I'd go with Gen III. Gen IV had some good ones, but the effect was lessened a bit by the fact that there were just so many of them...
Official Bride and Wife of Noire (of the Fire Emblem Awakening message board)
Gen 1 had Mewtwo. Since then I have had a few legendaries I liked the look of and gen 3 had a lot of good ones. However either nostalgia or badassery makes Mewtwo my favorite.
Add to that his awesome new form. Granted in future would that make Mewtwo's new form a gen 6 legendary or gen 1 because it is just a form of a gen 1 pokemon? I see Yveltal and the new mewtwo form basically making gen 6 my favorite depending on what other legends look like.