The biggest annoyance I've had here is that it makes some apps just plain not work if they're using something symlinked from ~/Library to ~/Documents (for Macku

The biggest annoyance I've had here is that it makes some apps just plain not work if they're using something symlinked from ~/Library to ~/Documents (for Mackup or other syncing solutions), though some work fine, so it may just be exposing apps that are doing something weird with file access in the first place.