Destiny is amazing, but I have one slight critique: The card frame should be an indicator of whether a card is a Hero or Villain. The only way to tell is the little rectangle on the bottom of the card, but it's so important for deckbuilding that it's easily overlooked. To make things worse, many of the Hero cards feature Villains in the art and vice-versa.

The old Star Wars Decipher game did this well. The Imperial cards were sleek and manufactured, and the Rebel cards were weathered and worn.

I just sort and store all my cards by Hero or Villain or Neutral.

+1 for referencing the old Decipher game - one of my favorite games ever.

As for determining what card is what faction, I agree it's not visiually intuitive instantly, but I've just been organizing my card by type and color anyway.

I just use an online deck builder. It allows you to sort by type, hero/villain, and color. Once I have my deck set, I just grab the cards/dice I need and good to go. I sort all my cards in numerical order.