They never said that. WinJS was just another possibility alongside .NET and C++/CX.

I think you're confused in a couple respects.

.NET has been their recommended enterprise platform for a long time. They came out with a JavaScript based environment for competition with mobile.

I think the state of the Windows Store shows that approximately nobody took that seriously.

Unfortunately there are a few libraries I use at work that were released around the whole Windows RT/JS debacle, so their documentation takes a little more figuring, and is frequently incorrect, due to only having code samples in these dead/orphaned variants.

I think part of it is that MS tied WinRT to full screen-only apps, a mistake they're fixing in Windows 10. Some of the features of the WinRT API look neat.