Factor #1: A requirements hurricane turbulently blew in one direction without control and consistency. It settled down in the 'eye of the storm', and then management said, 'Oh snap, we want it this way', and another turbulent hurricane blew in the opposite direction - without time or skill to change all the original requirements. These problems metastasize through all remaining steps of development.
Factor#2: Management said, "We need this big thing real quick. Lets get a big consulting firm to do it." Several firms gleefully responded.
Factor#3: Management told the selected consulting firm, "We need all of the big thing to go live at once, and remember we need it real quick." Big teams can be very productive, but only when they are carefully grown over a period of years. Quickly assembled big teams become a swamp that absorb money and grow weeds.
The $40-$50 million is just a down payment. Having built a kudzu swamp to serve an Internet market that is rapidly changing, the NYT will spend that amount several times over in the next 5 years to update it and keep it maintained.
We have at least 2 US companies building space launch capability, and several other international "space launch for hire" organizations are operating. NASA's Ares rocket development was a waste of money, and Obama was right to stop it. Let the commercial space trucking business competition get started, and lets try to get new US companies to be the winners in this business. Neil Armstrong is stuck in 1969, but meanwhile, "the times, they are a'changin'".