While admittedly, the yaoi genre seems to have been overtaken by a negative view due to fujoshis, the genre itself hasn't been stagnant. It's been evolving to the point that even members of the community find it easy to sympathize with the characters. Some have even begun to see it as a side of the same coin (with yaoi as the "more romantic" form and bara/gei-komi as a more explicit one) [there are scholarly articles on these by the likes of Thomas Baudinette and Nagaike Kazumi that explain this better than I ever could]. And I want to point out that while Yaoi has been predominantly made for females, it has also helped pave the way for LGBT content. It makes it easier for authors to circulate material to the general public and even provides people who wouldn't normally be into this kind of media with an introduction of sorts.
Anyway, that's my take on the academic discussion currently going on. But I think that the fact that yaoi is an evolving genre with various kinds of works is what makes it work as a tag in this site. Adding Bara/Gei-Komi wouldn't really help, in my opinion, since people can't often tell the difference and this is a relatively obscure subgenre. Not even the academic community can find a specific definition since manga is a dynamic media.
