It does give you a lot of options, but I mostly pick the relevant ones and ignore the rest. Just remember to choose the relevant "archive warning" tag and anything else is up to you.

And yeah, the tag system could use more standardizing, but I usually browse through similar fics and see what tags people are using, then slap ALL of them on my fic. (Ex. Tim/Kon, Tim Drake/Kon-El, Tim Drake/Conner Kent... it gets more complicated when the characters have multiple canon names.) It's definitely not a perfect system, and there's room for improvement, but I think it's pretty good compared to what's out there.