It doesn't matter if it worked fine before. If most users want to search for these tags then the tags have to stay.
Tagging does not exist in a bubble separated from searching - in fact, searching is the most important function in the site, because without it our database and tags become useless. If thousands of users find it intuitive to search for character tags rather than combination tags, then that's what we have to use. And can you blame them? A gentag combination will never be equivalent to a character tag when certain characters have multiple or even dozen different skins, all different from each other and all possibly conflicting in the case of gentags.
See artoria_pendragon_(all) swimsuit -artoria_pendragon_(swimsuit_ruler)_(fate) -mysterious_heroine_xx_(fate) -artoria_pendragon_(alter_swimsuit_rider)_(fate) for example. Imagine if we didn't have the skin tags - it'd be impossible to search for any specific design.
Other tags like bb_(swimsuit_mooncancer)_(fate) in fact have this problem, where there's three different designs under the same tag and you can't search for a specific one without adding two or three gentags. That's the farthest from user-friendly.