In the Pacific, we also did not really have a forward base from which to stage invasions, like we did in Europe with England against Germany, and the bombing raids against Japan had to assemble B-29's from many bases so coordination was difficult.
All of our supplies had to be moved by sea, which put huge demands on shipping and it was hard to protect all of those supply ships over such a big ocean as the Pacific. The Japanese were very well dug in to the islands they defended, and believed in the Code of Bushido - that to die for the Emperor was a glorious death and to surrender was eternal dishonor. In Germany, only the SS were that fanatical.
Since we had to rely on our navy in the Pacific for just about everything, what we lost at Pearl Harbor put us at a disadvantage until at least 1943.
I can think of at least three.
First, the Americans had to deal with huge distances in the Pacific. The various island they needed to invade were separated from one another by large amounts of ocean. So they needed lots of shipping and logistical planning.
Second, they faced much worse climates, or at least very unfamiliar climates. In the Pacific, they had to fight in jungles that were very hot and humid, with strange insects and unfamiliar diseases.
Finally, the Japanese fought in a manner much different from the Germans. The Japanese did not surrender much, did stuff like Kamikaze attacks, and did not treat prisoners very well.
The biggest disadvantage the U.S. had in fighting the Japanese was the type of warfare that victory necessitated. With hundreds of islands under their control, Americans were faced with the daunting task of seizing each one. This was a unique challenge, because, frankly, this had never been done before in modern warfare. The U.S. needed to land troops on, sometimes, pieces of rock no bigger than a small city, amidst obstacles of corral reef, then advance into thick jungle conditions, all the while, fighting an enemy who enjoyed air support, and entrenched in bunkers, tunnels and caves.
Just figuring out which ilsands were key to victory presented a quandary to American war strategists--and this is evidenced by the U.S.s unique solution to the challenge. There were two strategies the U.S. used: Admiral Nimitzs take each island in the chain that approached Japans home islands, and General McArthurs wither on the vine approach, to capture on the important islands, and isolate the other islands.
Just that the U.S. would actually use two strategies tells you about the challenges the U.S. faced. It is almost as if the top commanders couldnt decided on a strategy--so they decided to use both. Yet that the U.S. could use two ways to fight the Japanese tells you something else. Once the U.S. industrial effort hits its stride in production, American warplanners were confident of victory over the Japan.