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.
I agree with both posts 2 and 3. We often focus on securing the perimeter and identifying outside sources but we fail to see the dangers within. Military personnel are often under tremendous strain. Soldiers need both the proper support and the proper investigation. One weakness on a military base can be the personnel itself. Sometimes there are warning signs of an approaching problem. These signs should not be overlooked or ignored. On a smaller base, officers might have taken more time to investigate potentially problematic comments. Then again, perhaps not. Fort Hood was able to respond quickly and decisively to the incident once it occurred. Unfortunately, the incident took them by surprise because it was an attack from within.
The major vulnerability in the Fort Hood terrorist shooting was the internal refusal to recognize Nidal Malik Hasan's prior actions, associations, and conversations with other soldiers as potentially dangerous. Hasan had already been noticed and investigated for his participation online with radical websites and explicit emails with Anwar Al-Awlaki. Refusal to look at his record as a possible future motivation and instead chalking it up to acceptable deviation allowed his act to be unexpected.
As the shooting incident in 2009 demonstrated, perhaps the biggest threat to Fort Hood and other military installations was actually internal, from its own personnel, rather than an outside threat. Beyond that, I would say that Fort Hood faces the same challenges as other bases around the country. It is so big that it is difficult to secure the entire perimeter around the base. One can guard all the entrances, but someone who was committed to causing an incident on the base would have little trouble getting on. So the biggest threats to the base would be from individuals or small groups of people- i.e. terrorists. The fact that many military bases use non-military contractors for construction and other services might also be an opening in security.