It only makes sense that he is Scar's son: they look alike, Scar chose him as his heir, Zira treats him like he is her son, he acts like Scar is his father, etc. But the Disney poeple decided to change it when they realized that Kovu would be marrying his cousin!

Personally, I think he should have been Scar's son. It would have made the movie a lot more interesting. But that would mean he would have to marry his cousin, which is gross.