This is probably one of the bigger offenders with the parent task. Take, for example the enwiki preference statistics, taken today:
The only valid values here are monobook, vector, cologneblue, modern and the various minervas (which should be merged, see T171644: Clarify minerva preference name).
After solving the subtask, we could run the following query on all wikis:
DELETE FROM user_properties WHERE up_property = 'skin' AND up_value NOT IN ('vector', 'monobook', 'minervaneue', 'minerva', 'timeless', 'modern', 'cologneblue', '0', '2');