It was not melancholy, this was a different Lois and Clark, so the ending would be different as well.
With Clark arriving fifteen years ahead of Lois meant that he could learn about this strange new world and be comfortable enough in it that his transition to the 21st century would not impede their relationship.
So, who was the Government agent? Jimmy's dad?
Bittersweet wrap up to a thought provoking story. Why do I say bittersweet? Clark ages much slower than Lois. Eventually they will be lost to each other....