Rayquaza. Not gonna get into which is the most powerful or whatever. Rayquaza, to me, looks the most like what a dragon Should look like and I enjoyed it's story line. Though the Spear Pillar was annoying.
I would have to say Dialga. He(yes I refer to Dialga as male), was the first gen 4 legendary caught, has an awesome theme on PMD 2, and I always thought of him relating to the Temple of Time and the Song of Time on Legend of Zelda: Ocarina of Time and Twilight Princess, In fact, on the world my fanfics take place in, there is a statue of Dialga in front of the Temple of Time in Hyrule which is southwest of Sinnoh in the world that my fanfics take place in. Also, when Dialga sends Ash back in time on the 12th movie, I play the Song of Time on youtube during that scene, I tend to play zelda music during some scenes of that movie.
Its shiny form.
Its position as master of all weather.
Its non-shiny form being green.
Its serpent-like styling, and general finned/long style.
Its position as mascot of the best video game of Gen III.
Outrage + Hyper Beam. Oh yeah.
Rayquaza without a doubt I mean he's super badass and is also the only serpent looking Legendary Dragon Type and also is the only one who looks like an asian dragon. In close second Giratina who doesn't like a scorpion looking dragon creature he's so weird looking but in a cool way.
How does this voting thing work here on Bulbagarden forums? Am I a bit blind now..? EDIT: Seems I needed to reach a big enough post count! Sorted now.
However, I'd vote for Rayquaza who is my favourite Pokémon. There's just something about his design, that I absolutely love. I like all the others as well, with a special place in my heart for the poor frozen chicken Kyurem! He's so cute.