Black and White: Zekrom is Black, Reshiram is White.
Black and white 2: Is a sequel, so naturally it would be '2'.
Yes, but the X and Y axis is used for more than just 3D things.
Also, if we're going to get technical, the world of Pokemon we see has been 3D since Gen IV. Only now are we seeing 3D people. There's more things backing up the DNA idea, more than the 3D axis idea.
Actually, I'm prefering X over Y. For some reason I see them messing up the Bird thing, and making it part Dragon, like every other legendary since Gen III.
In case you've not noticed, every Pokémon game there is good and evil, and they still add an extra theme.
Crime Mafia
Crime Mafia pt. 2
Enviromentalists
Astronauts
and let's not for get, Pirated Ninja Knights of Camelot.