[Well, that's because this game is about operations and his is about tactics, clearly.]

The colors indicate different... factions? No. Strategies. Generally a deck wants two. The in-game excuse is that they represent different kinds of technology, but that's an excuse for different strategies.

For example: Force, red, is generally fast and aggressive, capable of dealing damage without entering combat or of bypassing slower units. Gold, Harmonics, is focused on defenses and improving units and Sectors. Psychic, Blue, mainly likes to have more cards in hand and to bypass combat entirely.

I could describe all of them, but for now: Color indicates Tech, Tech suggests overall strategy.