The first real problem is that the entire system was built by consultants. They were well sourced. Development Seed looks like a damn good team and includes some very strong open-source contributors with experience, including in government. But, risking a broad generalization, the consulting culture is not one of long term commitment, has a lot of churn in people, and tends to be very task-and-budget-driven. Very few such teams can say that the output of their team is a multiple of the individual skills. Little of it is inspired. This is a fundamental problem of the government procurement and fulfillment process as it operates on the complete opposite spectrum of startup innovation.
Another, rather upsetting issue, is of half-truths around openness. This is not an open-source project. Publishing code on Github is not social coding. I am sure some politician got a few pats on his back, but publishing source code for a static website on Github did not improve anyone’s life. Moving all of team’s development into public view and actively taking pull requests from the public should have been the very first and important step. To whomever is in charge: do it now!
As always, cultural problems lie at the bottom of things. These are the hardest ones to fix.