I don't think there are many villains at all who I think 'had a point'. In games they tend to throw away any sense of ambiguity by the time you reach the end. Even someone like Artorius, who starts out with a damn good point, ends up taking things to such extremes you can no longer consider his views seriously. I'm really struggling to think of any games where there is a legitimate battle of ideology, where it's kinda ambiguous if you're on the right side or not. Sometimes you get a villain with a good idea somewhere, but then they take it to such an extreme they lose all their credibility.

You know what? I... I'm gonna say Vayne Solidor.

Sure, he was selfish and power hungry. But he also wanted to take power away from the mysterious Occuria and put mankind in control of their own destiny. Becoming the new Dynast-King wasn't really over the top supervillainry in his case; it was a necessity to take control of history away from the Occuria.