Yeah, I agree that God is sovereign. He knows the beginning from the end and will do all of his good pleasure and his counsel and will shall stand.
Isaiah 46:10
Declaring the end from the beginning, and from ancient times the things that are not yet done, saying, My counsel shall stand, and I will do all my pleasure:
And we also know that it is not his will that any should perish, but that all should come to repentance. We know that if this is his will then he could definitely perform it, right. So logically then, why is it that some will perish? Isn't it because he set it up so that man has to make the choice?
It's been that way since the beginning. Adam had a choice to obey or not obey and so has all men throughout time since then. Pharaoh had a choice, Noah had a choice, Paul had a choice...He didn't make any of them accept him and obey him, though. Although, I'm sure he made a few wish that they had, it still ultimately came down to their own choice.