Having the option to finally separate the [core].opt settings and save them in their designated cfg folders instead of having one big opt file in the root folder (and having to browse through a wall of text to find the core you want) is great.
The similar handling for the save files also sounds great but there is a problem. Instead of separating the save files per system, it separates them by core. The issue with this is that there are a few systems that share multiple cores. For instance, there are 3 different N64 cores and all of them are useful. Lots of SNES cores too and i personally love to test all of them. But having the saves separated this way means you have to copy the contents of, say, the ParaLLel folder into the Mupen64 folder. This means a lot of duplicate files for no reason, that’s added bloat. Not to mention having to manually update the saves for the other folders by finding out which files were more recently modified and other similar headaches.
I think the saves should be separated by system. This way all SNES saves will be shared via all SNES cores, N64 saves by all N64 cores and so on. It’s much more useful this way.