Rayquaza vs Giratina | Bulbagarden
Though Dialga is my favorite of the three, Giratina comes very close. It's got an awesome and different design, has two Formes that change drastically in design and appearance, has an unique Type combination (One of the coolest and most unexpected, as well), and has a more interesting relationship with the other two. I loved all of its involvement in Platinum, too.
I like Rayquaza, don't get me wrong, but it's got a more generic design (Even if still awesome), a Type combination we've seen too much already, and is also one of two Ubers without a signature Move (Eruption and Water Spout aren't exactly signature for Groudon and Kyogre, but it always felt as if it belonged to them more than the other Pokémon that learn it, much like Meteor Mash for Metagross), which lets it down. It does have a much cooler Ability than Giratina's two Formes, but it still falls short.
Not sure who'd win a battle, but I think Rayquaza might be the most likely victor. Still, I gotta go with Giratina, as it's way more unique and interesting.