Hm.. I started my life with Pokèmon with Ruby, because I tend to favour a red colour over a blue one, and with the cover being as shiny red as it was, I chose Ruby. Even so, my favourite of the two legendaries of the games were Kyogre by a mile. Even though I haven't used the Pokèmon nearly as much as Groudon, I still like him better. Who doesn't like "underwater flying cows"?
The same with Latios and Latias. I couldn't get Latias by my self, so I had to trade it with one of my friends, but I think Latias looks so much cuter than Latios. Therefore my favourite is Latias!