Blue cards *hears horses whinny off in the distance* ... aren't the "Good guys" as one might initially think in Star Wars Destiny. It's not that red cards represent the dark side of the force while blue means light (which would be an easy assumption to make. Just look at lightsaber colors). No, blue cards *horses whinny again* ... represent those who are Force-sensitive and the powers and gear they tend to use.
As the game covers all eras of Star Wars, you can potentially have Qui-Gon Jinn teamed up from Rey or have Darth Vader use Kylo Ren's lightsaber. Whatever you feel would make the best team and the best equipment. It's up to you.
How will you be building your teams?