Part of the charm of the graphics for games of this time was that they were pre-rendered from 3d models. A simple upscale doesn't really do it justice. I'd try re-generating the actual models, then pre-rendering them again in higher res. That might look better.

Also the character portraits are pure nightmare fuel. You went from anime style illustrations to this weird semi-illustrated but with skin textures look. Gross. Those could probably be fixed with better prompting. But yeah, maybe work on the art direction part.

Edit: I guess the graphics are from 3d models? Maybe the textures just need updating then, or like, less upscaling since the original models were basically just flat colors for the most part.