A lot of people seem to be missing the point here. Pixel art is a visual style; just like cel shading, voxel graphics or realistic 3D common to most FPSs. That this particular aesthetic was borne out of technical limitations is irrelevant. All art styles had their foundation in something, some of those being technological advancements in ceramics, pigments or metallurgy.
Of course, certain art styles are more popular than others. If you're looking at this from the perspective of a commercial enterprise it might make sense to favor another aesthetic over pixel art. That, however, does not mean pixel art isn't a legitimate style.
I read the article and thought Blake Reynolds made some compelling arguments. However, I think he's also missing the point. I took a look at the game, Auro, that spawned this discussion and I wasn't really impressed. I don't think what we have here is a failing of pixel art but rather some poor aesthetic decisions.
The style doesn't work with the type of game that it is. More critically, he went for a pseudo HD pixel style. As he himself states, he wasn't going for a retro look, although it does hark back to mid 90s sprite-based PC games. But this is a style suited to larger displays, not the mobile screens for which it's been built. At that size those graphics just end up looking slightly off. And while the individual graphics look great, crammed together in the game the whole thing feels just a bit off.
Early in my design career I was taught one important rule: when you design something make sure it looks intentional. Go too subtle and you risk it looking like a mistake. That's what happened with Auro.
He might have actually had a better response if he had gone with the larger pixels of so many other games out there. In any case, he deserves credit for trying to be different.