You have a point. Upgrading and forgetting the old release is the most common scenario.But how often do people try to switch from v3.0 to v2.0 compared to how often people would have to copy save files across from 2.0 to 3.0?
However the games in development that just add new content without deleting old content are less than 50% in my experience. This one is one of those having some content in older releases which is not available in current release.
So some player like to play older releases again.
They are doomed to manually backup their persistent file every single time they switch, while without the AppData feature you would have to copy the save folder from v0.2 to v0.3 ONE SINGLE TIME when you install v0.3 FOR THE FIRST TIME, then the two releases would be totally independent and you could switch back an forward without any issue.
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If Ren'Py Developers thought that copying "game\save" (literally one Ctrl+C and one Ctrl+V in File Explorer) was a too difficult task for the typical user they could just have implemented their AppData feature with a PROMPT: "Do you wish to import your previous saves? [Y/N]", and most of all... "Do you wish to overwrite your local persistent file (created with v0.2) with the one in AppData (created with v0.3)? - Beware: you probably should not mix them! [Y/N]"
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If they think their users aren't tech-savvy enoug... overwriting their persistent file WITHOUT EVEN WARNING THEM is not the brightest idea to avoid them having tech troubles...