I agree. The majority of early 3D games, even on PC, look much better when they are not filtered. I always preferred Quake 1 and 2 than their GL versions, for instance.
All these textures were made without filtering in mind, that’s mostly why. The N64 is a bit different though. Some/most of the textures in N64 exclusive games are made with this filtering in mind, so the filter acts like the final layer to see what’s the artist intended. Some textures in Super Mario are supposed to be filtered in order for them to look correct:
Otherwise you end up with this:
No matter how much sharper the image looks without filtering, the textures are not supposed to look this blocky.
The issue with a graphics plugin that’s so old and inaccurate is that the filtering also filters stuff that it shouldn’t, like the 2D UI elements. Thankfully, an accurate plugin like Parallel RDP doesn’t have this issue.