In one part of your post, you repeated something of an urban (or Airbus) myth regarding the development of the Boeing 707. Boeing spent $16 million developing the Dash 80 prototype that led to the KC-135 tanker. They essentially bet their company on that investment. However, the Dash 80 and KC-135 were too small for an effective airliner, so Boeing had to invest a lot more money to build the 707.

The 747 was the losing design for the jumbo transport, while the C-5 was the winner. That was a paper design study. After losing the military contract, Boeing had to invest a lot of money to build the 747. The money Boeing got to help design their transport entry was minimal compared to the cost of developing the 747.

I agree that the Shuttle's high operational costs were a result of cutting its R&D funding. However, there comes a point where the higher R&D associated with a fully reusable design can result in higher actual costs per mission. Suppose they'd spent twice as much on R&D in order to cut mission costs in half. How long would it take to recoup the higher R&D investment? Would that number of missions be possible given the design life of the vehicle? Without hard numbers, it's impossible to say. Just like spending more money on higher efficiency HVAC equipment has to be economically viable*, spending more (in the case of the Shuttle, a LOT more) on R&D had to be justifiable.

*If the energy savings from higher efficiency don't save enough to pay for the higher purchase costs within a reasonable time, then the investment doesn't make sense. This is especially true if it'd take longer to recoup the investment that the equipment will last.