I have 3 favorites as of right now. Those being Serperior, Garchomp, and Mewtwo. Serperior is slowly starting to become my no.1, but i liked it since i picked Snivy all the way back in my very first pokemon game, White 2. I still have that very same Snivy, except now it's a LV. 100 Serperior sitting around in Ultra Moon, going completely unused. Anyway, i also like how great Serperior is with Contrary, (because it sucks otherwise, let's be honest) since with it, Leaf Storm gives +2 SP. Atk instead of -2. All in all, a true favorite of mine, especially its shiny.
In terms of Garchomp and Mewtwo, i've liked them for a lot longer, but they might not be Serperior level. I liked Garchomp because i was always enamored by it when other trainers used it in Gen V. Me being the unfortunate soul i was, i couldn't use one because i had White 2. Until i got Black 2 a few years later and got that glorious shiny Gible from Benga. The raw power i felt from Chomp was so great that even now i never stopped liking it. Anytime Garchomp is available, you'll probably find me using it. Fantastic stats, a great lineup of coverage, and a great typing to boot. Oh, and NO, i do NOT like Chomp just because of Cynthia. I'm not the biggest fan of her anyway.
Mewtwo, on the other hand, was always an enigma to me. It was the embodiment of what a Legendary should strive to achieve. Even when i didn't play the games yet and i knew about PKMN from cards and the show, i always thought it was cool looking, and it left me wanting more of this all-powerful psychic cat...mutated....thing.
I finally got to use it and Mewtwo was everything i wanted it to be and my expectations were surpassed. Its shiny is great with the green tail and eyes, its movepool and stats are flawless, and it has a great status among the other legendaries of our time.