i see this problem too. however, there's a difference between using pixels to 'be retro' and using pixels while actually giving a retro feel.
the big no is using pixels, but not having alignment, using actual, high-quality music made with actual string and wind instruments and stuff, ect.
basically if you just have low-res pixel sprites but everything else is whatever the forget, don't bother. terraria is kind of an exception but eh, even that still bothers me about it.
if you want to actually give a retro feel, look at games like Ripple Dot Zero and Freedom Planet. they do use pixel art, yes, but they also have 16 bit music, correct palettes, not too overboard for a Sega Genesis game, ect. they feel as if they're actually games you would play on a Genesis.