I actually do see a use for the final category of tags
Often I won't know the exact wording that is used when I'm looking to see if a question already exists, so I'll search by both the game tag, and the sub-category tag and then just a single keyword.
For example, I did a search for the Blood on Ice quest in Skyrim before asking for help with it, but didn't find the potential duplicate because the related question was titled How do I find the murdered woman in Windhelm? and made no mention of the actual quest name. If I had known better, I could just just filtered for something like "[skyrim] [quests] windhelm" or "[skyrim] [quests] house"
Of course, not many people think to search that way (I didn't at first), however with the number of questions being asked for some games (ie. diablo-3), I'm starting to find adding a second tag quite useful.
As a side note, if you do decide to keep the tags I wouldn't bother re-tagging stuff. If the tag exists, it helps the question get found in related searches, but if it doesn't, oh well no big deal.