Another problem in choosing an excessively high resolution with old games is that the world texture & geometry detail don't live up to it. So you end up with fine, sharp edges on low poly geometry and stretched (blurred) textures.
Stretching textures removes contrast and if you look at old games today and think they look bland, dull, and depressing, this might be why. In the past, playing at a low resolution, with textures (and filtering) to match that resolution, a bright texel next to a dark one is used to make glowing detail, like computer screens, electronic panels & switches, glowing eyes on characters and so on. Once you turn up your resolution and the GPU stretches the textures to account for it, the interpolation is going to give you a smooth gradient of shades somewhere between the bright and the dark pixel. Contrast is gone, and the gradient tends towards grays or other muddy & ugly colors. Your game looks depressing.
Combined with the fine edges, this just hilights the "lo-fi"-ness of the game. It hilights the lack of detail. It literally makes the game look worse than it is. It's like slapping a low res web cam shot on a fine piece of art in a sad attempt to create a fake scene. It looks bad and does a disservice to the art.