I've become kind of fond of Deoxys mainly because of the effort I put in to translate her text in order to understand it. It surprisingly cute when you actually read it and not to mention but because of how Deoxys works as a Pokémon, her inconsistent design due to the ai's limitations is actually explained.
A second place for me is Darkrai purely off of personal bias. The fight was a fun concept and her personality is a lot more feisty and bratty then the other legends, which makes her stick out.