I've always thought that Vitani was Kovu's sister. It makes more sense, SBS has already cleared that up. As for Zira, Scar could've just been using her for an heir (Nuka) But he wasn't good enough so Scar just gave up and was killed before he could make sure he was getting another heir... And Zira was heartbroken and went to someone else or something, and the result was Kovu and Vitani... Then she went mad.
Makes sense xD I'd go on about Kopa some more, but to be quite frank, I'm bored with it. You don't support him as canon, and I do. Believe whatever you like, it's MY Lion King, YOU'RE as rightfully entitled to an opinion as Simba is rightfully entitled as King.
My "Zira" theory is they wre madly in love with each other, and Scar partly wanted to take over the Pridelands for Zira and for revenge on Mufasa. He didn't take his pride as (as you can see clearly) they are too scrawny and weak, so he gathered the hyenas instead. I think it was then Zira was impregnated with Kovu/Vitani, and Scar became furious with her. They fought about this. Soon after Scar died and Zira felt horrible for all those nasty things she had said and now she seeks to fulfill Scar's wish. But she died (I do NOT think she survived the fall into the river). I like this theory because it fits nicely into the time slots ^_^
Added to this, I think EITHER Zira knew Scar wasn't fond of Nuka, or she was being protective of Nuka and wanted Kovu to become King since he beared the most resemblence to her beloved Scar.... or what her Beloved Scar wished he would've looked like.