Yeah I'm not sure how to feel about where the critical plot is heading (although interviews with the showrunner seem to suggest that there are some big twists ahead), especially considering how the nature of the conspiracy has changed. The guy who created the show was kicked off after the pilot was filmed over "creative differences", and you can basically tell why - in the pilot they apparently engineer a train crash to kill one guy, and in later episodes the conspiracy seems, at least on the surface, to be a relatively small-potatoes affair, it's white collar crime crossed with espionage, basically. They don't seem to have the grand Deus Ex-style plan or frightening power they apparently had in the pilot. There are apparently other minor details that have changed from the pilot to subsequent episodes.
As a matter of fact, if you're curious at all about Rubicon I would advise starting with the second episode and go from there. It takes until the third or fourth episode to gain steam, but The Shield this ain't. It's a meticulous show.