LONG JOURNAL AHOY. Just my thoughts

Okay, so whilst I was on the train today, I had time to think about this whole Scar and Zira thing a little more How sad am I haha.

Anyways... right, my theory is now this, which kinda makes sense, not really from the point of view of the film story, but from the point of view of Disney (and it's screwups lol).

Kovu was originally going to be Scar's son, which would make Zira Scar's wife and Nuka and Vitani Kovu's siblings. However, this caused complications obviously in that it would have made Kovu and Kiara related. Whilst this is common amongst real lions, the characters of the Lion King are personified, and so it would be kinda gross lol.

So, they changed Kovu to being an adopted son of Scar, but due to the tight budget (LK2 was created in the Australian studio, which was well known for direct-to-video sequels which are considerably lower budget than their blockbuster counterparts), they didn't really have the time to fix the relationships of the rest of the characters. You'll probably find they had some sort of deadline for the design/storyboarding/scriptwriting stage, and most likely didn't have the time to work out all these kinks.

And so, because of this, Zira should "technically" be Scar's wife, and Nuka and Vitani are still "techinally" Scar's children.

Yes, people assume Vitani is Nala's kid, yada yada, but this simply isn't true because Disney has a fantastic trend of designing characters according to their personalities. Vitani has blue eyes purely because of the fact that she is a good character... she needs a "trademark" good colour to somehow show that she is a good character, which subconsciously alerts us in the beginning. But since this small feature is overshadowed by her "evil" looks, we don't outwardly register it. It's just like the fact that Kovu is a dark lion, however he has a rounded chin which is a trait of good male lions. He also has a "shine" in his eyes, something Scar nor Nuka has (as Nuka remained loyal to Zira till the very end).

We also need to think of LK1 and LK2 as two completely unrelated films. For one, they were made by totally different people in totally different countries (despite the second film having roots in the main studios, but not alot), and two, when they made the first film, they hadn't planned for a sequel at all. When they made the Lion King books with Kopa, the people in the Australian studio who wrote the script had probably never even heard of those books which were created in the USA by some dude who had managed to get some subsidiary Disney publishing company (NOT the people who made the film) to grant him the rights to slap their name on the cover before they even thought about a sequel, and they thought that having a female protagonist would be a great change in LK2 (explaining why Kopa wasn't in the film, nothing to do with Zira killing him or whatever).
And so, because of this unrelatedness between films, we can dismiss the fact that Scar was shown to have had no relationships in the first movie, and that he tried to come onto Nala (which was a deleted scene, so the creators of LK2 probably didn't even count that).

So, I think it's safe to assume that Nuka and Vitani are most definitely Scar's children since they were never fixed to fit in with when they changed Kovu, and that Zira WAS Scar's wife. What we REALLY need to be wondering then is... who are Kovu's parents? Perhaps he was raised by Zira to believe she was his mother? Idk. At least we have the rest figured out

Yah, this is all down to Disney screwing up lol.