OK, now with that out of the way, there are some complex underlying issues that the film tackles, if even in an only surface manner. Can a machine possess moral judgment? It's a mistake to think that this movie is another Terminator wannabe, because the machine isn't necessarily pure evil. What makes it complicated is that its learning behavior from humans; specifically, it's learning from a bunch of macho, type-A, egomaniac humans, namely, Navy pilots. If anything, the EDI just calls out the pilots on their own ego-driven bull. Who sets the conditions for when it's OK, or not OK, to obey orders? This is the central problem since the humans set a bad precedent by endangering civilian lives in an early mission on a risky maneuver with no logical reasoning behind it; the EDI simply learns from human behavior and sees itself as more capable of following orders and striking available targets.
While it doesn't encompass much of the movie, it drives the controversy that the machine can have a moral complexity that matches that of a human being. The EDI reasons, bargains, cheats, and lies, and if it seems confusing to an audience, it's because the EDI is a little too human in that regard. Of course, to really buy into the premise of the whole movie (like why they didn't just put a master kill switch into the thing to begin with), you'll have to turn your brain off. But like I said, you won't miss too much 'cause stuff blows up real good.