This is why shovel knight looks and feels like the old classics it’s imitating. They artificially limited themselves to color pallets and some technical limits that old systems had. I think they ended up using 18 colors instead of 16, and double the sprites on screen, among some of them. Indie games usually just go with what looks good and use modern limits because they can. Most the time it’s not a choice, they just do what works and that’s ok too.
There’s a more comprehensive breakdown from yachtclub themselves here I was off a bit in my specific examples but overall they do a good job breaking down why their game fits and breaks the mold with lots of examples. The game is a lot more faithful to NES than the vast majority of indie pixel art games. There were a few late-gen NES titles that are relatively unknown but look way more detailed and complex than the typical NES game too.