I'm sorry, but I can't just choose one.
Moltres: We already have a fire/flying pokemon, it's called Charizard, and he's a whole lot better than that Legendary.
The Three Legendary Dogs: Why? Because they run away. Sure that adds onto the difficulty on catching them (unless you have a pokemon that has Mean Look), but I like a pokemon that stays put...plus these three are shameful clones of the legendary birds.
All the D/P Legendary Pokemon. To be quite honest, there's way too many Legendary now. Sure they're strong and rare, but there should also be few of them.
I honestly think they should stick it with the Five Legendary Birds, Mew, Mewtwo, Rayquaza, Deoxys, and that new Fighting/Steel one.
I have a great idea (one that would get me pummeled to death). To make them truely feel legendary, how about make them non-transferable between cartridges? Oh you can transfer the information to complete your pokedex, but you can transfer Mew to a friend. Make them rare by not having soo many options of having them distributed.
But if I had to choose absolutely one, it would be Moltres. My favorite? Articuno.