One of the first things that I feel should be done is to set up categories for the tags. Here's a few that work.

Artist - The tag. for any artists who worked on the piece.

Characters - A list of any characters that appear in a piece.

Copyright - Any particular source material used/parodied in the piece, like persona_5 for the Jon head on the shirts Ann for example. Other possibilities would be the_runaway_guys for any TRG-specific pieces, etc.

Tags/General - Normal tags simply describing the content of the piece.

Meta - Tags describing the piece in relation to the booru itself, such as tags for unusual resolution like lowres, highres, absurdres, etc., tagme for undertagged pieces, translation_request/translated for if there's foreign text to be translated in the art, and so on.

I'm not sure exactly how this is done, but it's an important way to help clean up and sort the tags on the images as the booru grows with Jon's stream.

There are a few tags that are duplicates of other tags but with slightly differing word choice or spelling. Ex. Alternative_Universe vs. Alternate_Universe. Any help to clean up small things such as that in order to clean up the tags and make art more easily searchable would be appreciated.

One way that I know of to simplify the slightly differing tags is to alias them to each other so that if your search for either of them, images containing either tag come up. For example, "Jon" has already been aliased to "Protonjon" so if anyone searches for Jon, the search will include all posts tagged with "Protonjon" as well and vise versa.

The big problem with this is of course that someone has to alias each of the relevant tags, which could be a very big job. I don't know if there's a better solution, but that's the one I know of.