Enhancement:

[DylanSchneiderman]

If you want a vanilla modpack, have a button that deletes a folder at a certain location called "Vanilla" (C:\User\Factorio\Vanilla is what I'm using to explain) runs factorio with the target of "factorio.exe" --mod-directory C:\Users\Factorio\Vanilla. This way it always uses a empty (actually the term is just-created-a-minute-ago) folder as the mod directory and as such will only have the base mod loaded.

[kalisjoshua]

I don't think creating, and deleting, a folder is necessary as the only thing that needs to change is the mod-list.json. What I was planning on doing for the "Vanilla" option was to make a persistent "pack" that simply disables all but the "base" mod in mod-list.json.