Empire of the Sun gets my vote as the best operational/strategic level simulation of the Pacific War.
It is so very different from the European theater, with many of the operations (especially before late 1944) small in comparison to the European theater--and in discreet geographical areas.
You also mentioned the War in the Pacific: Admiral's Edition computer game. I would love nothing more than for someone to design a modern version of that game with a good UI and a friendly AI to help you plan and move your forces without the excruciating level of micromanagement required. I don't have time to devote to the level of micromanagement required in WITP: AE. But I've sent transport ships to pick up an Army regiment, found out that the transport ship was too big for the port level, or the ship didn't quite hold enough troops... so found another transport, moved it the forces, then ran into a problem because my bombers conducting a pre-invasion bombardment were bombing from too high... So frustrating.
Wars are conducted by staffs, and a good friendly modern AI helps players focus on the important decisions and enjoy the game. Just my 2 cents...