Older pokemon including certain "legendary" pokemon that really shouldnt make a return for new games such as X and Y.
Celebi and Jirachi - they have no place to fit in X and Y. Yeah Celebi and Jirachi had only like one little subplot in HeartGold and Platinum if they were Gamestop specials.
the roaming legends such as Raikou, Entei Suicine. They had their fun in HeartGold.
The Swords of Justice in White 2/Black 2. They had their own little thing going on in White 2 and Black 2.
Giratani and Diagla and the other one. They were Platinum pokemon that were important for the storyline in Pokemon Platinum. As for them being in X and Y, they just wouldnt be cool anymore other than just filling up the pokedex.
Ho-Oh was the like big main legend in HeartGold. Just wouldnt fit in anywhere at all in the current X and Y games
Both Mew and Mewtwo have been done enough as they keep ending up as cave pokemon every game such as HeartGold, Fire Red/Leaf Green, and I dunno about Platinum though but HeartGold mostly
They only appeared in the games that expanded their history and they only appeared in two gens which one was a sequel to. Mew and mewtwo haven't appeared in any other game side storywise until now.. Also x and y is the perfect game for mew and mewtwo to reappear to end their story. Arceus and the creation trio have a place in this too.
Understand that there is no joy. Cry, that there is no eternal punishment! Where there are new fans, there is money. I, myself, cry for you humans!-Nyrathothep