What is the reasoning behind some of the allies, in 6th edition Warhammer?
I'd say the reasoning behind the allies matrix is 60% fluff, 10% balance, and 30% Matt Ward lolz. 

A lot of the matrix is what you would expect from reading the basic fluff.  Guard working with the other imperial factions and with a few of the others to represent renegades.  Tyranids can't ally with anyone because they would just eat them.  Tau will work with anybody if it will advance the greater good.  There's been some talk of the Emperor giving instructions to certain Marine legions to protect a certain alien race(hence the Marines and Tau being battle brothers).  And the Eldar/Dark Eldar works a little better if you consider one part of the pair to be Eldar Corsairs instead of true Craftworld or Commorragh Eldar. 

The fluff is in a state of flux right now.  The Matt Ward authored codexes have done a number on established cannon.  This is behind some of the weirder combinations you see in the matrix.

I think game balance was secondary to fluff when deciding who gets to ally with whom.  Otherwise the Tyranids would have at least one ally option.