I think people were expecting the 12" to be the "new Air" and follow the same path as the original: start off as a premium-priced ultra-portable but evolve into the new entry-level. The (just) "Macbook" name suggested that, too.
Only Apple knows what the sales were like. They did have a bit of a pile-up at the low end with the 12" MB, the Air and the entry-level 13" "formerly known as non-touchbar" MBP (which is arguably the real 'Just MacBook' rather than a 'Pro').
I think the issue with the 12" is that Apple clearly want to position the iPad Pro as 'more than a content-consumption tablet' so the two products are really in contention, especially with touchpad keyboards, mouse support and full Photoshop lined up for iPad.
The new Retina 13" Macbook Air is more like the 12" MB than the 13" MBA it replaced as both use the Y-series 7W CPU. In a way, what you described is exactly what happened, just with a name change.
I agree with you that Apple's naming conventions lately have been a mess, especially with the non-touchbar MBP. I also agree that the iPad is being positioned as Apple's premier ultraportable, and not any Macbook. I think that is why Apple ultimately up-sized the Macbook a bit and called it the new Air.