I've actually got an idea using the B-29s and the nukes for a scenario. Something along the lines of BoG now where the story is woven and your actions dictate the outcome.
The push is on taking and capturing the fields on islands to island hop to Japan, while maintaining B-29 bombing runs on the cities of Japan. If the US forces take the fields they need, if they push so far ahead they have no opposition, the end result is the bomb gets dropped and the war is over.
If the Japanese forces sink the invasion fleet supporting the island hopping campaign, or if they shoot down enough B-29s over Japan, the loss will cost the allies dearly, as the final frames near/over Japan will have more defenders. The pressure on Japan's war machine would not have been enough to break resolve, and they push back. Also, perhaps designate a ship/fleet that the nuke is being shipped onboard. If it gets sunk, that nuke is lost and it sets the next frame's spawn point further back.
You could do a whole lot with this, assuming that tokyo map still works.