My only experience is with Windows, so I don't know if this applies to other OSes. However, the installer is certainly unique to Windows, and that is where I see the problem.
When one installs an upgraded version of the player, there is first an uninstallation of the preceding version. For the uninstall, the default is to preserve the existing VLC profile (i.e., preferences, etc.). That makes sense. However, for the following installation of the new version, the option to remove the old profile is checked by default. That seems wrong to me, not only because the uninstallation and installation are inconsistent on this issue, but also because deleting the profile would cost me a lot of work that I went to in order to customize keyboard shortcuts and other things. So far, I have noticed the checkmark and unchecked it; but I would bet that many others, having noted that by default the uninstaller does not delete one's profile, did not worry about it when going into the new installation and thus had their profiles wiped out unnecessarily. It seems to me that the safe default would be to preserve the user's profile. In fact, I see no reason for the option to even exist in the installer, as the option to remove the profile already exists in the uninstaller. In my experience, most installers (e.g., those from the Mozilla folks) will happily adopt an existing profile without even asking about it. So, even if there must be such an option, its default should at least be to preserve any existing profile.