Emulator

Fixing upscaling issues is a fairly difficult proposition. Some effects may not be able to be upscaled, and even then if they are, it's arguable whether it's the job of the emulator.

My feelings are that if the emulator does support higher resolutions, it should do its best to make them work well.

As far as I know there's no good way to fix this, although you could try raising the texcache accuracy. Other than that, there's technically no way to provide upscaling with accurate EFB copies. The only reason it works in some cases is because we currently have one huge hack to make it work anyway, but making it work is either impossible or a huge amount of work.

This isn't going to be addressed by any of the active developers, so marking as WontFix.