I think our perception of popularity is influenced heavily by the experiences others have had and relate, as in forums like this. So it depends entirely on the measure of popularity you're looking at.
The measure that matters to the manufactures is how much they sell. If they ain't on the shelves, they can't sell them.
But another odd influence is popular culture. People make themed builds now so the aesthetics of a motherboard have to fit with the aesthetics of whatever's popular so that it can be fit into a theme. To someone more interested in the hardware and it's capabilities it seems odd, but that's one way manufacturers addressed the impending death of the PC market several years ago.