I guess I'd like to know who was responsible in the government for budgeting this project. Some names would be good to know so we can point some fingers.
Not familiar with the military contracting model...you can pm me if you like as this is off topic

Is that where you bid and even if takes you 7x the budget you only get paid for the original bid? The X amount not to exceed Y amount model?
Military projects are just famous for going over budget. For much of the same reasons, particularly for new-inventions. You know how it is. Engineering something from nothing is a lot harder than bidding a new road or something. You have to invent stuff as you go. Not to say the techniques aren't "standard" in most cases.
I think they did some stuff OK. For example they used a large CDN. What they didn't do was a gradual roll out (like Press 1st, curiosity day 1, etc. then by time zone or something). Would have eased the load.
Looks to me like they needed a lot of beta testing yet and revisions. Probably ran into a schedule wall. THAT is nothing new either.
The funny thing is that the site is fairly nice looking. And the information is not badly presented. There's just...questions...people have and some if it may be due to state-specific sites too. The whole "state's rights" thing looks like it messed the project up. If they had just said "Do it this way" and everyone was the same they would have been efficient. No. They have 3 different models (at least) and the state chooses.

So for some states you just get kicked to the state site, I think. For some, it's a standard site (maybe still state specific, IDK). For others, it's the Fed site. So that's 3 different ways to implement...State-run, State-uses-fed model, Fed-run.
As I understand the articles. Don't really know any of the specifics so I probably shouldn't say much.
It's the 50 fiefdoms thing. Totally doesn't work for any economics of scale. "A kingdom divided cannot stand". Grrrrrr. Jefferson would be happy. Total chaos, but each state got it's way. The anti-fed people just make things 50 times harder than they have to be (or more than 50 due to territories).