The old way of having contracters compete with designs and the loser getting $0 isn't possible when costs are this high. You need a guaranteed market or nobody will participate.
The F-35 was the result of such a program. Lockheed and Boeing were each give a billion dollars and a set of requirements and told to make the best plane possible.
Capabilities are not inevitable. You have to create R&D programs to bring them to fruition. Is the complaint here that its rolled up under the same line item?
It's a recipe for every ambitious, failed research idea to look like a clusterfuck boondoggle.