I personally want to the Tree to be a story element and not a Pokemon, but that's just me.
I think it's likely the Squirrel will be the Pixie of this gen...
IDEA HAS CHURNED:
Player starts out in home town, and sees a squirrel, meets professor, asks about it, they don't know, but think it may be... nevermind. They continue the journey, and the Squirrel always appears in or around a place where the Serpent is influencing people as its minions (the evil team).
Eventually, you learn that they have captured one of the two guardians of the great Tree Pokemon (Grass/Ground maybe), the one of your game game, and are going to sacrifice it to the great Serpent. The Squirrel takes you to the tree, where the guardian mascot of the opposite game appears, and picks you up, taking you to where it is being held. You fight through the evil team, and battle your mascot, which is angry and has turned against you. You have two options, KO or Catch. After that, the leader of the teach laughs, and captures the other pokemon. Cutscene where the Legendary Serpent comes out of the ground, and the just KOed or Caught pokemon knocks it out of the way, saving them both. You then have to defeat the Serpent as the final battle, which is a tripple battle where the Squirrel, you, and the opposite legend all right the Serpent, which is defeated for now. You go to the tree and the other guardian returns and thanks you, and says he will send the squirrel if he ever needs his partner if you captured it, or they are both there.
Pokemon Z, the Serpent has awoken again, and the region is dying. One of the guardians has gone missing, and the other has been captured by a new ground of villains. In this game, unlike the last, the team takes control of the Serpent, and has used it to capture the Pokemon that lives within the Tree. The quirrel once again guides you, and you are able to capture the serpent this time around. Post Game adds an additional storyline where you must find the Squirrel and X and Y, who awaken the tree for battle and capture.