I think the classes are not overshadowed by the subclasses, as far as capability goes. It was actually a strong consideration during the design of the game. Now, as far as popularity goes, sure there are a lot of folks out there intrigued by the concept of a scout instead of a thief, or a pyromancer instead of a magician, but it is mostly because they want to explore concepts that they would enjoy playing and role-playing. From a mechanical standpoint, the classes cannot be discounted as less than the subclasses. Of course, we had the benefit of hindsight, after decades of playing AD&D and seeing the power-creep in the subclasses presented in The Dragon (yes, I know, many were intended to be NPC classes, but we all used them BITD) and also the subclasses presented in UA.
HYPERBOREA- A Role-Playing Game of Swords, Sorcery, and Weird Science-Fantasy