I spent some time this evening going through the tags on SuperUser, and considering the wider audience it attracts, which are much more inexperienced the ability to edit tags gets abused quickly. This could also be due to the lack of understanding of what tags are altogether.
Keeping the tags on SuperUser consistent is also made harder by the wider topic range. Therefore we quickly end up with duplicate tags being added to a question, or even have users putting spaces in tags not realizing it creates separate tags.
Looking at the tags list the last 10 pages are tags which has been removed but are still available for selection. It is going to take some time to clean this up, and with users adding new one's the minute they get tag editing rights, it seems to be a endless exercise.
I would suggest the limit gets increased to at least 2000 if not higher.