Some schematics have certain blocks like stone, it would be great if we could chose substitute blocks like instead of stone we can have cobblestone etc.
A alternative would be for schematic creators to choose what blocks can be set to other blocks, although this would not work as well as the original idea since it would not work with non litematica schematics

Do you just mean replacing blocks in the schematic? That can be done in the Schematic Rebuild mode (which is a bit badly named and will likely be renamed to Schematic Edit mode). There is a wiki page about that feature here: https://github.com/maruohon/litematica/wiki/schematic_editing

There is also some kind of system planned for "valid substitutes", so that you can basically configure which blocks are allowed in place of another block, for the renderer and/or the material list and/or the verifier. Also the Rebuild/Edit mode still needs some improvements, for example allowing to change a block type while keeping all the properties.