If you look at the cost the calculated originally for the Skylon, it doesn't actually beat Falcon 9 even.
And when I listened to some presentation with the people involved, it seem they had no real understanding of some of the complexity involved. Their history is mostly in academic and British space industry, and all the project they worked on before are canceled paper studies that were kicked around in Britain.
When asked about the structure of Skylon the answer was vague hand waving about some new materials that might exist. Nothing at all concrete that has even begun being tested for high complexity air frames and high requirements.
Elon himself was asked about this when he presented in Britain. And he answered by saying that investing massive amount of complexity in the easiest part of your flight was counter productive.
Pushing the thrust of your traditional rocket engine a little bit higher, is far, far easier then engines.
And if you are really optimizing to that kind of extreme, doing even more advanced version of second stage engines and structural optimization on the second stage would likely always have a higher pay off per complexity invested.