personally think, the Gray Mascot could possibly be Cobalion, as it could give as a "Fresh Start" that Gen V loves to do, as predictable Mascots are getting annoying. For this idea, Milstration Cave is unable to acess until the End of the Main Game though, by talking to the man outside of the cave, he will give you TM Rock Slide that was previously available before the E4.
If that were to happen, N would get Reshiram and Zekrom. Before the battle Cobalion would come (as it heard about Pokemon liberating and it wanted to see for itself) and you two agree that N is way too powerhungry thus you (attempt) to capture Cobalion and then you fight N. Cobalion also has his Gray Exclusive move, Recover.
Afterwards, Ghetsis will laugh (instead of Scolding N) as this was his plan along. The tention of the Yin Yang Pokemon caused his God Stone to activate, thus summoning Kyurem (God Forme) then you battle him.
After the credits, you can get Terrakion and Virizion (with the new Gray Exclusive move Extremespeed/Aura Sphere respectivally. By bringing the 3 of the Musketeer Pokemon to the statue of the Elite Four (the one that glows when you beat the 4) and talk to it, the statue will rise instead of dropping down to Alder. You will find many pictures of the Trio and then you will se a big portreit of Keldeo. Alder will come and will tell you about the story of the 4 Pokemon and then tells you that Keldeo lies in Hoenn Seas. He gives you *insert name of Ticket here* that will bring you to Pacifiglog town. Then, by Diving, you can see Keldeo's aquatic lair and fight him (He has Gray Exclusive move Energy Ball)
You can also go to the Dragonspiral Tower to fight Reshiram (Gray Exlusive Move: Nasty Plot) and go to Milstration Cave, Cobalion's old location, to fight Zekrom (Gray Exclusive Move: Swords Dance).
Then, at Hoenn, after catching the 2/3rds of the Tao Trio, you can go talk to N, who is in Pacifiglog Town thinking about his life. He will then battle you one final time, he then tells you that Pokemon are amazing Pokemon. He hints that he will stay in Hoenn (Replacing Wally for RS Remake :3) and he tells you that Kyurem is in the Plasma Base. He gives you the God Stone aswell.
You go to the Plasma Base in Castelia City and talk to the Elevator. Instead of bringing you up, it goes down. It leads into a Frozen Cidadel and the God Stone flashes, summoning Kyurem.