Considering this is a game for the 3DS, X and Y may represent the dimensions, and because of this I agree that the name may be Team Z, to represent the third dimension, or Team Naught, to represent any variable.
My guess is that they will attempt to create a dimension that is their own, rather than try to take over the current world (much like Cyrus did, destroy the current world to create his own, rather than take over it).
I hope they make this a little more mature, like having to sacrifice the Legendaries to obtain their power, rather than just have them get absorbed for a few minutes (like Kyurem).
But, my guess will be that, if this comes up, Palkia, Dialga, and Giratina will make an appearance, being the three Dimensional Pokemon (Palkia is the 3 dimensions, Dialga is the 4th, and Giratina is the reverse dimension), or if it's DNA, it's going to be Mew, being the ancestor of Pokemon and containing DNA of all of them.
And going further to support my theory about the villians going for the dimensions, X and Y are the legendaries, the bird being Y and the stag being X. Since X is run (the stag runs across the land) and Y is rise (the bird using the second dimension with freedom), it would follow that they'll try to make a Z pokemon.