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I've no opinion on Zygarde yet, but I do like Yveltal.
For all generations, my favorite legendaries come down to: Mewtwo, Groudon, Rayquaza, Arceus, Tao Trio (Zekrom, Rushiram, & Black/White Kyurem), & now Yveltal.
if were talking gen 6 then probably yveltal. if in general then arceus deoxys latios and latias. if only the gens ive played then deoxys latios and latias
If it's only X/Y, I'd say Yveltal or Mewtwo because they're both awesome, although Mewtwo isn't is powerful as he was in the older gens. However, if it's Gen 1-6, I'd say Lugia. She's powerful, plus she's very useful for taking down Fighting-Types (Possibly my favorite type, but still) except for Lucario.
Celebi is my favorite legendary of all, but out of then Gen 6 pokemon, probably Xerneas. It's cute imo and blue is my favorite color. I would've loved to like Hoopa, but it's design doesn't do anything for me. I kinda wanted it to be cute like Diancie.