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I prefer Mewtwo, not only because it was the original 'uber legendary', but it's still perhaps the strongest Pokemon in Pokemon history. And that's not something to take lightly!
Going back to the Red/Blue version pokemon games, I remember how when I was real little, everyone used to make up these BS cheats on how to catch it...
Suicune. Well, it's because he's beautiful and I love how he purifies water. (Raikou makes thunder and Entei makes volcanoes blow up, that's really helping everyone, isn't it?) And he's like a wolf, and I love that. And I've just always loves the way he looked.
Luiga seems the coolest to me. I don't know why. Probably because the first Pokémon game I played was Pokémon Silver. Though I don't like it's not a Water-type.