Yveltal wins this one for me. As soon as I saw him, I wanted Y to be my main version. I've always had a huge fondness of Eagles, and his connection to Norse mythology made me even more interested. The Dark/Flying typing sealed the deal, I am a huge fan of Dark types.
My second favourites are currently a tie between Xerneas and Hoopa (Can't decide which one I like more ATM). Although I like Yveltal more, Xerneas is still mighty impressive and majestic. I love all the colours on it and again the connection to Norse mythology is really interesting. Xerneas is actually my favourite generation 6 Fairy type.
Hoopa is one of those Pokémon I really didn't like at first, but he really grew on me later on. Confined is super adorable and his mischievous antics appeal to me a lot. It is my favourite Ghost type of generation 6. I like Unbound Hoopa quite a bit as well, his monster like appearance is very effective, plus he's a Dark type. But I won't lie, he has one of, if not the creepiest cries in all of Pokémon. Hoopa also has interesting powers and he looks to be inspired by mythology too.
My least favourite generation 6 legend is probably Zygarde. I just find him OK, I'm not super impressed with him, though I do like the connection to Norse mythology. His new forms haven't won me over, 10% in particular looks really out of place.