The difference with Chang, Ru'afo and the Borg Queen: the focus of the story in these films was not about them. You can remove these characters and the main story is still intact.
Khan, Nero, Shinzon and Soran are these Bond type villains because the story focuses solely on them. If you remove them, the story falls apart.
It's okay to have a villainous character in your story, but it gets tiresome if he is the focus of it.
It doesn't always have to get tiresome. TWOK is still easily one of the best trek films there is. The problem, of course, is that it almost seems like they've forgotten how to do anything else. And that, often as not, they don't even do this particularly well. Soran, Shinzon and Nero would, imo, rank among the worst (not in a good way) villains I've seen.