Big military projects have the additional problem of congressional interference. Congressmen regularly force military acquisitions that the military may not even want or need in order to funnel dollars to their home districts. So it might make more sense to build all of the components of something like the Joint Strike Fighter in the same state, but instead it's spread over something like 40 states to ensure the project's survival.
And for whatever reason, the military seems to have a very short memory when it comes to major weapon system procurement failures. "Hmm, the V-22 went over budget, killed a good number of people, has higher maintenance needs and operating costs than we anticipated because of the USMC's requirements. I know, why don't we tie the entire future of our combat airpower to the JSF and hamstring that project with the needs of the USMC..."
Long story short, the space constraints of operating from an amphibious carrier forced design compromises on the V-22 that significantly worsened that program. Now with the JSF, the same thing is happening with the VSTOL variant that the USMC wants.