At this point, the two have become mechanically pretty dissimilar, because it's now built around aspects of PrecinctOmega's Horizon Wars rules. The similarities are more in elements of the style, focusing on a small number of highly customisable protagonist characters (to an extent more than most skirmish games do).
As I said, I think probably the neatest thing is the idea of NPCs controlled by a card deck - it doesn't necessarily make them intelligent, but it does make them unpredictable, and that has its own advantages. It means players do have to be prepared for the unexpected, rather than just exploiting an overly formulaic system. (Frequently a problem in video games, where you can get so used to how the AI works that it's again effectively just a stupid machine again).
