I just finished the episode where Ed goes undercover as Krill. Easily the best episode thus far. Largely because it is the strongest story driven episode to this point. It had the typical McFarlane pop culture jokes, but they took a backseat to the drama.
Further, this is the episode that I feel finally distinguishes this from a Star Trek knockoff (which it becomes when it stops being parody). Trek is idealistic to a fault. On Star Trek, Kirk would've found a common ground through the Krill scripture that talked them out of using the bomb, or come up with some other crafty plan to save the day. That didn't happen here. Instead Mercer had to kill an entire ship. And while he saved children, he was strongly rebuked, being told in no uncertain terms that he simply spared a future generation of enemies.
That's when it hit me. This is a much more nihilistic version of Trek, but the nihilism is balanced out by McFarlane's levity so it doesn't become overbearing to the audience. If that is the voice of the show moving forward, I am very excited about it.