After watching last night's PC gaming show, I would agree that OP has a point in a way.
I don't think there's anything wrong with the style itself and it can be used to great effect in certain games. But I think it's a fair argument to say that indie devs lean far too heavily on it for the nostalgia factor and it's a bit too much. I don't want every other thing that comes out of the indie dev scene to be just another pixel game because certain games would work far better with polygonal graphics. Especially 3D shooters. There's honestly no excuse not to make a game that features polygonal visuals because the tools and assets available these days make it just as easy as making a pixel game.
I would be really interested in seeing more indie FPS games that try to go for the early 2000s PC shooter aesthetic instead of preying on older gamers' nostalgia by imitating Doom and Quake. It was a quaint and endearing idea when Dusk showed up and it was followed by a couple of other copycats but right now it's slowly turning into an annoying fad and it needs to stop. There are still some occasional standout games like Prodeus or Selaco but why do these games insist on using 2D sprites despite boasting pretty impressive special effects is beyond me.
Like, for example, I recently replayed some older shooters on GoG, including Star Trek: Elite Force 2 from 2003, and that game still looks pretty great:
Everything animates smoothly, the movement and controls and super tight, and the 3D graphics and texturing still looks pretty good if you ask me. Throw in some dynamic shadows and you have yourself an impressive looking game made on a small indie budget. None of that 2,5D pixel art jerkiness and jank. Why don't these indie devs try to go for something like this for a change? At this point it should be just as easy as making any other boomer shooter.