The best route for practically all users is probably fsck -y.  Yes,
there's a tiny chance that a) fsck will break something AND b) that
something happens to be important to the user AND c) the user could have
done better manually BUT d) they didn't bother backing up AND e) they
didn't know that the default was fsck -y and change it manually.  The
confluence of all of these is far less likely than one being missing,
and if one is missing then fsck -y is better than plain fsck, or fsck
-p.  Yes, the consequences of fsck -y failure are more serious than the
consequences of fsck -p failure, but the latter shouldn't be neglected
and will crop up *much* more commonly, especially as Ubuntu becomes more
mainstream.

You could add a scary prompt by default, but this will terrify ordinary
users and not be very useful to most power-users either.  I think
running fsck -y instead of fsck -p by default on Ubuntu Desktop is the
best way to fix this issue, with a well-documented way for power-users
to alter the setting to the more conventional fsck -p.

-- 
Command-line recovery required when fsck reports an unexpectedy inconsistency
https://bugs.launchpad.net/bugs/58430
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