OK, answer me this: who in the organization has the technical know-how to decide how to solve all the SEO and usability issues; and the authority to do so?
If there's nobody even close, then they will have massive spec churn.
Actually the NYT has a pretty sweet tech lab with a crew of guys very knowledgeable about this kind of stuff. Some of the stuff I saw in there was years ahead what I've seen elsewhere.
Of course, actually getting buy in from the organization as a whole is the hard part. Technology is always the easy piece.
Again, I am not disagreeing - there are certainly tons of things that can factor a major price increase - whether it's outside consultants, tons of meetings to iron out office politics, getting input from all stakeholders, etc.
But at a $40 million price tag, someone somewhere is either dropping the ball, or someone is taking serious advantage with billing far more than reasonable for their services.
If there's nobody even close, then they will have massive spec churn.