Isn’t it better to keep it hidden though? Normal users shouldn’t really be messing about inside those folders directly. The GUI offers control over both ignore patterns and versioning already, so I’m not sure if there is any actual need for keeping them visible. More advanced users, who need direct access, won’t have problems accessing hidden folders anyway.
On the other hand, if the top .syncthing folder is hidden, there’s not really any need to hide the subfolders, is it?
How about something more like this?
/.syncthing/ # hidden
|
+ folde-rid01/ # replaces .stfolder, folder marker
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+ versions/ # replaces /.stversions
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+ tmp/ # stores all temp files, per #2208 <-- for consideration, implemented later
|
+ ignore.txt # replaces /stignore, default ignore file
However, there is also a problem with those, whose .stfolder is a file rather than a folder right now (although it could probably be automatically converted), and also those that use custom folder markers, which is a much bigger problem, because you cannot really store any Syncthing-related stuff there.
I’m not sure if there exists an issue on GitHub about this, but there have been some discussions in the forums for sure. There could be a variety of use cases for having different ignore patterns for the same root path, e.g. like my own in https://forum.syncthing.net/t/solved-large-index-size-with-nothing-synced-but-a-lot-of-ignores/14284. Also, they would be useful when sharing the same folder with different people without wanting to give them access to everything.
Syncthing can do this already 
(without different ignore patterns). You can add the same folder even 100 times, and it will work, with understandable performance impact, that is.
Backward compatibility will be a huge problem with this one, won’t it? There surely are some users with very funky custom folder IDs currently 
.