I've been watching this for a while and I find it funny. You're fighting with windmills here.
Saves stored in the system folders are a normal thing, after all it has the advantage that if you upgrade the game build, you don't have to move anything manually. If the saves are under the dev name, it's not that bad. Most developers, however, are not even able to set this up and the game gets lost somewhere under the "DefaultCompany" folder or something, or worse under some working title.
Also you forgot the worst possible location - registry.

Simple arcade games using just registry, like money value = x, item/stage.. 1 unlocked = True/False.
Later builds of MGI have a gallery, however they are full scenes as they are in the game, with all the dialogue. It would be nice to have only clean scenes with easy switching between parts, so the player could just enjoy the scene and not have to click through the whole story... or as you said the RenPy-style skip function.