Thematically, the NC and VS have the weakest lore for fighting one another in the game. No mater how you look at it it's either the NC are bigots against the VS or the VS are transhuman supremacists against the NC.
Mostly the VS are despised by most players because the vast majority of them CONSTANTLY spam max units and easily have the best (and most obnoxious) MBT in the game. Let's not mention the long history of gen dropping.
The NC and I have had our ups and down over the years, and many of them may not have the tactical ability of a gerbil, but I still prefer them over the VS anyday. I would dare say the NC have had some of the absolute best and the absolute worst players in the game. Plus blue and gold look sooo much better than purple and teal (and black and red, though the TR do have a good look.)
Now and forever!
Edit: Blah, of course it's a necro. THIS is what I get for not reading past page 8. My point still stands though, however many years LATE it is.