@Quazwalt  
Agreed, I once thought the NC was for freedom and liberty but wouldn’t they stop fighting after a few months or a year? I mean look at most Revolutionary Wars in the world, they always had cease fires for peace treaties and agreements. I don’t think the NC is out for freedom…

Well, how the hell else are you going to get peace? Hell, it’s a time tested empire that’s stood for a millennium without war until you and that Vanu rabble tried to usurp us.  
Of course you’re assimilated under their banner, up until a couple of years ago it was the ONLY banner to be under.
 
And stop pretending the New Conglomerate is a force for freedom, they’re nothing but a bunch of corporate shills out for their next buck, and their using YOUR work to attain it.

*by force

terran pepublic…. peaceful….
 
MWAHAHAHAHAHAHAHAHAHA  
the terrans are an opressive totalitarian government. they want to stop the fighting force and by stripping you of your standarts and freedom and assimilate you under their banner.
 
the new conglomerate believes in freedom at any cost and fight said opression. they rather die free than live enslaved
 
the vanu are just xenophilic cultist nutjobs

I think:  
Applejack and Pinkie Pie = NC  
Applejack because she’s the kind of person I associate with the NC mentality of the average Conglomerate terrorist (redneck)  
Pinkie because the NC is pretty damn chaotic and so is she  
Rarity and Twilight = VS  
Rarity because the Vanu is friggin fabulous and Twilight because she’s sciency and so are the VS.  
Fluttershy and Rainbow Dash = TR  
Fluttershy because they’re very orderly and peaceful and she just wants people to stop killing each other  
Also, if you think RD isn’t TR, you need to remember what element she represents.
 
In conclusion, loyalty until death.

In short, I thought.  
Rarity, Applejack=TR  
Pinky pie, Rainbow-dash=NC  
Fluttershy,Twilight-sparkle=VS

I personally thought that applejack was more of a TR character myself. (but I was dividing the mane 6 characters into groups of 2, and assigning each group to each empire)