I was eager to say Charizard but looking back, it truly is Charizard... Even though Y is the first game where I actually got to use it in one of my teams, when I used to play with roms, I used Charizard in Red, Yellow, FireRed, switched one of my pokemon in Silver for a Charizard too... Also, I chosed Charmander in HGSS already thinking of having a Charizard. Now, I use the one I chosed in Y as my main Pokémon and use it mostly as Mega Charizard Y and after getting the Shiny event recently, I intend to use this new one as my main Pokémon in the next game(s) (Z or wtv it's going to be), probably more as MegaZard X to contrast with the former...
Other than that, there's Giratina who was the first main member of one of my in-game teams, since Platinum was the first game I actually bought, and I tend to choose it over the other 2 dragons whenever that situation presents (like in the HGSS Arceus event).
Lucario is the only pokémon I've used in more than one team, other than Charizard, so that could count too.
Actually, I'm also using Kyurem in both Black 2 and White 2 (one in each respective forme).
Finally, even though I'm reusing all my old Emerald team between OR and AS, Rayquaza has a special consideration (I used it before getting Emerald and I even got a Kyogre from HG just to get the Rayquaza in my SS game).
I've always had a thing for 3rd Game mascots...