I remember in the late 90's and early 00's it seemed like SSTO launch vehicles were all the rage and they were even building the X-33, then suddenly nobody wanted to talk about SSTO vehicles anymore. What happened that made nobody interested in single stage to orbit launch vehicles anymore?
Interest was lost mostly because R&D money dried up, and also because the shuttle proved that reusability was difficult and expensive.
SSTOs generally have worse payload fractions than staged launchers, with no inherent advantage in exchange. In the later portion of ascent, after burning most of its fuel, an SSTO is carrying significant mass in now-empty fuel tankage and now-overpowered engines; a two-stage rocket has left that mass behind.
If you're designing a reusable launcher, SSTOs are attractive because you only have to recover one part, but then you're adding the mass penalties for a reusable on top of the mass penalties for SSTO -- thermal shielding and either aero surfaces for a horizontal landing spaceplane (like X-33) or reserve fuel for powered vertical landing (like SpaceX). Cost-effective reusability is challenging enough to design as it is, without the physical constraints of SSTO.
By contrast, a two-stage fully reusable launcher needs far less thermal shielding on the slower-moving bottom stage than on the upper, so you only carry the heavy thermal solution on a small part of the entire launcher, and you get to drop some dead weight along the way. As SpaceX demonstrates, you can also develop this capability one piece at a time, but there's no such thing as a partly reusable SSTO.
Skylon may be able to offset some of the SSTO mass penalties by taking oxidizer from the air, but to make the most use of the air-breathing mode, it has to fly a lower ascent trajectory -- which means more heating, thus more mass penalty in its thermal design.