The Vanu are that odd one out, that's true. But in a good way - they add the alien space element to this sci-fi game.
It's a tried and tested approach to sci-fi backgrounds, and it works (see Earth 2150 for example, or even better Battlestar Galactica).
The Lore:
There's a
top-down faction, that believes in peace through control and organization (TR, or the military in Battlestar Galactica).
There`s a
bottom-up faction, that believes in peace through diversity, freedom and empowering the individual (NC, or the civilian leadership and the workers unions in Battlestar Galactica).
And there's a third faction, that sees current humanity as ultimately flawed, and believes in peace through altering humanity by using an
external factor, for example with (alien) technology. (VS, or the Cylons in Battlestar Galactica).
How the Lore is implemented with respect to the Vanu Sovereignty
The Planetside universe has something of a Cold War theme to it: Here the "bottom-up" liberal corporate-democracy faction, there the "top-down" centralist state faction, both busy making war with each other.
And now "the scientist" find something so powerful it makes nukes look like firecrackers. Instead of risking the threat of total annihilation, they decide to defend their findings and work towards a more enlightened humanity.
And this "Let the alien artifact get into your head and you'll find peace" part is where both TR and NC go "I won't let no alien mess with my mind. I'll rather die a human. For humanity!"
The Design
Of course, there's also the simpler answer: Without Vanu, Planetside 2 would just be a near future shooter. While this might appeal to the Battlefield/Modern Warfare crowd, it would totally leave out the Mass Effect fanboys and Sci-fi nerds. That's why everybody needs the Vanu. Without them, it wouldn't be a space game.
Or to sum VS up:
