You commenting this makes me question if you really know what you're talking about. What you just said has absolutely nothing to do with the engine the game was made in. Ren'py just stores saves in appdata, so if you delete the game and reinstall it it will find the saves. But that applies to a lot of games in a lot of engines that save games in a lot of places other than the installation folder. Not to talk about games with cloud saves, but that's another matter.
personally, I'd rather the saves were stored in the installation folder so when I'm done with a game I can just delete everything, not have a ton of files I don't know about scattered about roaming appdata, locallow, local, my documents, saved games, etc. often times under folders with the name of the dev making it even more difficult to figure out what's what.
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.
So long as the game provides for a reasonably quick way to get to the scene I want to get to I guess the details don't matter. The individual scenes in MGI wouldn't be too bad if you could more rapidly go through dialogue like you can by skipping in Ren'py or other VNs. ANd I think the main game does have a gallery, havent' played in a while so I"m not sure.
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.