The main point of using tags is to categorize questions, either to help people searching for particular questions or to help people selectively focus and ignore active questions based on their interests.
For this reason, I'm not particularly fond of sunni, since it's so all-encompassing; even under the umbrella of "Sunni Islam" there's not a whole lot of unity in a lot of matters.
Tagging by madhahib (e.g. hanafi, shafii) does make a lot of sense here, since there is a fair amount of cohesion within individual madhahib, but sunni is more of a class than a category: It would apply to pretty much any post that any of the individual madhahib tags would apply to, which just clutters up the tag space. We only get five tags per post: Make them count.
And of course there's also groups that fall under the umbrella of "Sunni Islam" that don't necessarily follow any one particular madh'hab, which may attract the sunni tag simply as a catch-all because there's no other real way to categorize them.
This is particularly problematic for questions which don't focus on a particular madh'hab. If a question is legitimately asking for what "Sunni Islam" says about a matter, that's inherently relevant not only to sunni, but hanafi, shafii, hanbali and maliki. That's all five tag slots used up already, and we haven't even tagged it about anything the actual question is about. Or you can just tag it sunni and force everyone looking for hanafi etc. stuff to search multiple tags in order to find it. Neither seems an optimal solution.
The general wisdom is that if your question needs more than five tags to be effectively categorized, you probably need to spend more time focussing your question. Don't even get me started on stuff that just asks what "Islam" says.
I could make similar arguments against shiism, but right now it's almost exclusively used for Ithna Asheri Shi'ism, being the most dominant form of Shi'a Islam in practice. Maybe it could use a rename (shia-ithna-asheri or shia-twelver, maybe?) but as used, it seems to be fulfilling its purpose of categorizing things so I'm not really worried about it.
For sunni to really work though, at least as it seems to be used now, it pretty much needs to be added to almost every post that is relevant to Sunnis, which would pretty much be any post that isn't already tagged with shiism (this is probably a bad idea, since there's about seven thousand of those).
I…really have no answers here. But it is a problem.