Firepower maybe in the IJN favor, but manuever is a function of how you employ your forces. I do not see how you can automatically credit the IJN superioirity. Care to share how you came to that conclusion? Interior lines of communication may be all well and good, but if the issue is taking PM, that does not apply, and ship speeds are pretty much the same on both sides.
Take a look at the skill levels of Japan's ships vs Allied ships at the start of the game. The USA is sadly lacking in skills, especially at night. Both sides have some quality aggressive surface commanders that negate each other. The Allied have the edge with Radar AND Damage control, but the ships available until the Enterprise and Hornet show up are not terribly effective overall.
Any Allied ships coming to PM are under Japan airspace. Japan can sit back on the other side near Lae and demolish the port while being completely out of reach of Allied CV's. Japan has a very short term fuel advantage (very useful now that CV's don't fly aircraft without fuel).
You asked why I think Japan wins on ships:
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AFTER ACTION REPORTS FOR 05/08/42
Weather: Overcast
Night Time Surface Combat, near Port Moresby at 10,40
Japanese Ships
CA Myoko, Shell hits 3, on fire
CA Haguro, Shell hits 1
CA Aoba, Shell hits 1, on fire
CA Kinugasa, Shell hits 4, on fire
CA Furutaka, Shell hits 2
CA Kako, Shell hits 2
DD Shiratsuyu, Shell hits 3
DD Shigure, Shell hits 2
DD Yugure, Shell hits 3, on fire
DD Ariake, Shell hits 4, on fire
DD Akebono, Shell hits 2
DD Sazanami, Shell hits 4, on fire
DD Ushio, Shell hits 4, on fire, heavy damage
Allied Ships
CA Portland, Shell hits 19, Torpedo hits 1, on fire, heavy damage
CA Chester, Shell hits 11, Torpedo hits 1, on fire, heavy damage
CA New Orleans, Shell hits 6, Torpedo hits 1, on fire, heavy damage
CA Astoria, Shell hits 9, Torpedo hits 2, on fire, heavy damage
CA Minneapolis, Shell hits 5, on fire
DD Sims, Shell hits 2, on fire
DD Anderson
DD Hammann, Shell hits 2, Torpedo hits 1, on fire, heavy damage
DD Morris, Shell hits 1, on fire
DD Phelps, Shell hits 1
DD Dewey, Shell hits 3, on fire
DD Monaghan
DD Aylwin, Shell hits 1
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Night Time Surface Combat, near Port Moresby at 10,40
Japanese Ships
CA Myoko, Shell hits 2, on fire
CA Haguro
CA Aoba, Shell hits 1, on fire
CA Kinugasa, on fire
CA Furutaka, Shell hits 12
CA Kako, Shell hits 3
DD Shiratsuyu
DD Shigure, Shell hits 4, on fire, heavy damage
DD Yugure, Shell hits 1, on fire
DD Ariake, Shell hits 2, on fire, heavy damage
DD Akebono, Shell hits 2, on fire
DD Sazanami, on fire
DD Ushio, on fire, heavy damage
Allied Ships
CA Portland, and is sunk
CA Chester, Shell hits 2, on fire, heavy damage
CA New Orleans, Shell hits 17, and is sunk
CA Astoria, and is sunk
CA Minneapolis, Shell hits 13, Torpedo hits 3, and is sunk
DD Sims, Shell hits 13, on fire, heavy damage
DD Anderson, Shell hits 1
DD Hammann, Shell hits 25, Torpedo hits 1, on fire, heavy damage
DD Morris, Shell hits 2, on fire
DD Phelps
DD Dewey, on fire
DD Monaghan
DD Aylwin, Shell hits 18, on fire, heavy damage
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Day Time Surface Combat, near Port Moresby at 10,40
Japanese Ships
CA Myoko, Shell hits 1, on fire
CA Haguro
CA Aoba, Shell hits 2, on fire
CA Kinugasa, Shell hits 2, on fire
CA Furutaka, Shell hits 2
CA Kako
DD Shiratsuyu, Shell hits 2, on fire
DD Yugure
DD Akebono, Shell hits 2, on fire, heavy damage
DD Sazanami, on fire
Allied Ships
DD Anderson, Shell hits 3, on fire, heavy damage
DD Morris, Shell hits 3, on fire, heavy damage
DD Phelps
DD Dewey, Shell hits 5, on fire, heavy damage
DD Monaghan, Shell hits 1
Thats roughly normal, with both being given good commanders.
) is the abandonment of PM beginning at turn one. I've heard reference to it as "Fortress Australia", ...
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