Primal Rayquaza (always loved the basic one, don't know how to describe its awesomeness), followed by Primal Groudon, Mega Latios/Latias (almost the same anyways), Mega Mewtwo Y, Primal Kyogre, Mega Diancie (Fabulouussssss), and Mega Mewtwo X. Though I'm sad you didn't consider Lucario as (at least) a semi-legendary, even though it's an evolution... :3
So heres a little touching story. There once was a lad who derived from an Emerald world, he conquered and plundered, but alas his time came to an end. He sent his creatures far and wide, some came back, some would hide.
Travelling between lands they were sent to a newer world, one they hoped to call home. They settled about but were quickly thrown. They aided in many battles and quested mightily in these newer world lands. One stood out above them all.
He was the mightiest and the bravest. They revered him, and named him Rayquaza. This amazing creature fought all and always won. Even though his original master was long gone, he still stood strong. Rayquaza traveled with his fellow friends and even some new ones along the way. Hoping that one day he can return home.
Although he was only half way through his journey his persistence never quit. His master's Blaziken kept him company and together they made each other strong. Generations of heroes and battles have passed. Albeit a half a dozen. Finally he is near to his home. Soon he will return to his land of origin, and gain a new power. This creature has endured a lot, but will finally end his journey.
I've had my Rayquaza since Emerald, and have sent it across dozens of games and files. Sent it all the way up to Generation XY. He has helped me through numerous battles, 3 leagues, and even faced off Red himself. Now I am going to be able to Mega evolve it in it's land of origin. For a creature that isn't alive, it holds a dear place in my heart. Thanks for listening.