Maybe I've just watched too many episodes of 24, but I would think a major weakness is the vulnerability of the soldiers. I would hope none of them would fall to economic pressure, but soldiers are vastly under compensated and a simple bribe might be enough to cause a problem from the inside... from people who understand the workings of the base itself. It wouldn't be the first time in history that a bribe has caused someone to betray their comrades. Additionally, family pressure could come into play. Again, playing on the mid-level people with a working understanding of the base, a kidnapping could cause a morally incorruptible person to betray his country to save his family.