The short answer is there's probably not an easy way to clean up your appdata folder. CCleaner focuses mainly on registry issues and outdated software (Happy to be corrected since I haven't used it in years) and not on saved files.
It's also based on the fact that most people here would've played VN's on both Ren'Py and Unity. As soon as you do that, you create at least two different directories in AppData (C:\Users\<User>\AppData\Roaming\RenPy in addition to the save files in the 'game' directory for Ren'Py VN's obviously but Unity could have directories in Roaming, Local or LocalRow depending on the VN which contain more than your standard save directories). The more Unity or other engine (Eg RPGM) games you play, the more directories you create making it harder to clean. So generally it depends on how many VN engines that you've played on with Ren'Py being easier to clean. If you've only played using Ren'Py then you don't need CCleaner to clean it up.
For the save folders, generally what you're saying is yes to both engines but if there's a code change or re-work, then your save folders will be useless to hold and you'll have to start from scratch or find a new version save through the game threads.
