I might be getting too far ahead of myself, here, especially since I don't even know if I'll be able to buy the game, but I think it's probably Alola ninetales now.
I say "now" because for more than ten years, gardevoir has been my pokemon; the one I wanted with me everywhere; she hasn't been completely dethroned yet (mostly because I don't know ninetales' more technical details), but the fact that after having her for so long, and even after her becoming a fairy type, ninetales made me consider her not being my signature pokemon anymore, when others like mismagius, meloetta, glaceon and articuno couldn't, is significant enough.
Together they would be best, but there can only be one, sadly.
Besides, it always felt weird not having my favorite pokemon be of my favorite type, anyway.
My signature Pokemon would have to be Purrloin, love the design; and I like how in the anime they had Purrloin be the honest Pokemon despite its species being known for stealing things in the Liepard's-eye Jewel episode, showing that you shouldn't judge a book by its cover.
Despite what my username says, my signature Pokemon is not Victini, but Shaymin! More specifically the Shaymin I've had since Pearl. I always add her to my team post-game and she cleans up everything. Also, Shaymin is my favorite because it's adorable and can kick butt at the same time! Also, I love how radically different the Land and Sky Forme's personalities are. And the Sky Forme's design is just perfect.
If we're talking about non-legendary or mythical Pokemon, then that honor would have to go to Swampert. My all time favorite starter and my oldest living Pokemon (Had him since Sapphire!), coming full circle having returned to Hoenn in Alpha Sapphire. With a sweet new mega evolution to boot!
At Nationals 2014 I kept hearing people talking about my Clawitzer and Sylveon combo, and Clawitzer has remained a staple on my team.
I just have an obsession with it tbh, competitively it's my favourite Kalos Pokémon. My signature would probably be Noivern if it was competitively viable.
A toss up between Slowbro and Jellicent.. I can relate to Slowbro the most, for there's nothing better then lazing on the beach with no cares at all (That tail has got to be havy so can you really blame him?) Love Jellicent for its deep sea spookiness. Always have been fascinated by mysteries of the ocean.
It's a shame using them both on the same competitive team results in a massive disadvantage because they basically have the same strengths and problems.
I like using all Pokémon equally, but my signature Pokémon depends on the Generation. In Generation I, it was Raichu. In Generation II, it was Feraligatr. In Generation III, it was Gardevoir. In both Generation IV and Generation V, it was Magnezone. In Generation VI, my signature Pokémon was Greninja. With Generation VII, I've found myself a new signature Pokémon in Alolan Raichu, though it may also return back to Magnezone again.
I like all pokemon, it's rare that I find one that doesn't seem interesting to me. However, if we're talking spirit pokemon (and in some cases we may be) it's Braviary. Always Braviary. Just love the lore, the movepool, and sheer amount of fun I've had with him.
I have a weakness for flying types though. In no particular order, Noivern, Dragonite, Honchkrow, Braviary, and occasionally Pidgeotto for some reason. It may have to do with in Blue, my second game, Pidgeotto eclipsed my Wartortle by Lavender town. My rival was served by a Pidgeotto that never finished evolving for some reason. Then my Blue Cartridge fell into a bucket of water, wiped the data, fried the internal system, and now saving the game does nothing. Good times.
Back when I first started playing on Yellow, my signature was Pidgeot. Always had one, and always named him Abe. No idea where the name came from, but every time I played Yellow, Abe would join my side.
Later on, in Silver, I was raising the Eevee you get from Bill at like, 22h00 (10pm), and all of a sudden it evolved. I was so confused! Umbreon was all of a sudden there. Ever since then, I've been particularly fond of Umbreon. I would go as far as calling it my Signature Pokémon.
If I had a signature trio, I'd say it would be Umbreon, Pidgeot, and Sceptile. Not for competitive or anything, but for personal adventures.
Blastoise has been (And always will be, mind you) my signature pokemon since my cousin traded me his Squirtle from his FireRed game to my Emerald game. I would always nickname my Squirtles "Spoopy" because that was the name of the one I first received. In almost every Pokémon game I've played, I've attempted to receive Squritle (or anything in its evolution line) at all costs, which at one point meant getting a pricey GameShark device for my Nintendo DSi. He was always my favorite Gen 1 starter and will stay so when I buy Sun and/or Moon.
Tl;dr, who needs a fire breathing dragon when you have a turtle with flipping water cannons?!