I never got into 1st edition, but my friends were pretty big into it back in the day. Though I didn't play, the faction colors really bugged me. Green for Baratheon? Yellow for Lannister? No. So I'm thinking of giving 2nd edition a shot when it comes out later this year, and was delighted when I read the following blurb from the Nate French's letter...
"We decided that there was room in the game for more than 6 factions, and are expanding and adjusting the color pie accordingly ."
As we've already seen, card color for Tyrell and Baratheon will be green and yellow, repsectively. It looks like the Night's Watch will be black. Presumably Stark will be white or gray (I'd prefer the latter), and I'm guessing Greyjoy will be some shade of blue and Martell will be orange. That leaves the Targaryans. They were the culprits behind the messed up house colors in the first edition. Barateon had to be green because Lannisters were yellow, and Lannisters were yellow because Targaryans were red. I'm thinking they'll be the something else so that the Lannisters can properbly be red this time around.
So the question is, what color will they be? We'll find out eventually, but for now I'm guessing they'll be...tan? That's Essos enough, even if it doesn't fit a strictly Targaryan faction. So yeah, that's going to be my guess.