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We actually bypassed many Japanese garrisons on islands that we didn't need to either occupy or reduce completely.  Late in the war it got so that the Navy would use the bypassed islands as firing ranges for training gunnery and aviators before they sailed into their operational areas.  On the way to the front, they'd stop by and shell or bomb one or two of these for practice.  Anyway, most of the islands we actually landed on were because we needed a base on that particular island.  Some of the landings turned out to be unneeded because the war took a different turn, or some bad decisions were made, but there probably weren't too many islands that were stormed that didn't need to be.

As for the chemical question, it was FDR's policy not to use chemicals.  There was some resistance to chemicals on the JCS early on, which started to change as the war progressed.  There was also a fear that if we used chemical weapons on the Japanese, the Germans would use that as an excuse to use chemical weapons in Europe.  No one wanted to go down that road.  Chemical weapons were available, on supply ships with the invasion forces on all of the invasions in case the Japs used it on us.  Chemicals got stockpiled during various landings and not too well kept track of, and that has caused problems with disposal once they get discovered.   Once the Germans surrendered and Truman was in office, with the high casualties of Iwo Jima and Okinawa, the military was more receptive to chemical use and most references show planning for it's use in the invasion of Japan.

As the war dragged on and the high casualty reports were coming back in, the Army Chemical Corps began various programs to investigate just how useful chemical weapons would be.  The programs included not only conventional chemical weapons, but biological ones that were focused on crop production, and fire of course.  The Chemical Corps developed several weapons that were designed to be used on crops to cause famine within the Japanese homeland, and were operationally tested on some of the bypassed islands that were so easy to use as firing ranges.  The bypassed Japanese garrisons had taken to growing their own food, since they had no other form of supply.  So the Army attacked the crops with various chemicals to see the results.  Results of that type of chemical attack took a long time to show anything positive.  It worked, but it took months to actually get any effect.

Because of the delayed effect, the anti-crop weapons were never used on the Japanese homeland.  Due to timing, it was figured out that we'd probably already be on the islands before the cycle could actually do anything, so occupation and feeding the captured populace would be hampered.  It just simply took too long for the anti-crop stuff to work to make it worth while. except on the "target range" islands.

As for Mustard Gas, etc. they used the same bomb containers as the fire bombs did. So any actual bombing with chemicals (back then there were only a few ways to effectively deliver chemicals) would reduce the firebombing champagin's capability.  Since the firebombing was going on at such a level that they actually ran out of containers, there was very little left over for chemical bombing, if the desire was even there.  For the planned invasion, container production was increased so that both firebombs and chemicals could be supported.  On the surface, it would seem that pumping gas into the tunnel complexes would be perfect, but testing found that it just didn't penetrate far enough into a tunnel complex, so it didn't do much good in some situations.

So you basically had a situation where the command structure didn't want to use it until late in the war, there wasn't much reason to use it on bypassed islands, and you would really complicate your own situation on the ones we had to land on, and it gave less than optimum results.

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If the Japanese were isolated on islands, why didn't we use chemical or biological weapons against them? Was it treaty? It seems that if we ended up using "the bomb" we may as well have used some mustard gas. A few hundred thousand mice with the plague would have wreaked havoc on the Japanese garrisons. I know that this wouldn't have worked on the bigger islands, but what about places like Iwo Jima or Tarawa? Just wondering.

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Thanks for this informative post - did not know about the anti-crop efforts.  +1 on the disposal problems:  The Army is still finding gas munitions at Schofield - some apparently left from the first World War!!

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You realize there were non-combatants on a lot of those islands?