Villain has the same hangups that Villainess has, but that didn't stop anyone from thinking it was an okay tag. I agree of course, that Villain wouldn't work. There's already a lot of manga with villain leads.
"Evil male protagonist" wouldn't work because the protagonists aren't evil. They've just inherited the role of an evil character, despite their good nature.
Something along the lines of "Reverse Antagonist." Something that isn't gender specific.
If we're talking about the male counterpart, then "antihero lead"?
All the context for the "Villainess" tag is in its description, so any new tag could just have its context there, as well.
If folks are desperate to cling to "Villainess" then changing it to "Villainess/Villain" would be tolerable I guess.