re: Why wasn't Peleliu and other islands bypassed?

Don't discount the desire for retribution against the Japanese at every turn possible. There was, to some extent, a desire to be PUNITIVE for what happened at Pearl Harbor. That desire probably led us into taking islands at the time that history suggests weren't strategically important enough to warrant what we spent to take them.This wasn't a cold, mechanical war of numbers against some faceless enemy. The Pacific campaign was, in part, a war of payback and there was some real hatred for the Japanese and a desire to make them suffer at every chance possible.

Hell, look at what LeMay did to the home islands once he got within striking distance. If you ever wonder why Japan is such an ultra modern society, it's because a large number of cities were just burned to the ground when LeMay got there and heaped scorched Earth warfare on Japan. They're modern because most of the old cities literally did not exist after 1945. Look at Tokyo before and after LeMay. He was methodically firebombing every city he could and had he not been expressly forbidden by his superiors to bomb certain cities, there would have been no untouched cities left to drop nukes on. LeMay would've burnt them to the ground before the bomb was ready and we wouldn't have had any pristine cities left that would be able to give a before/after comparison to show the world the utter devastation our new weapon could inflict on a city.

To some extent, LeMay definitely wanted to make the Japanese PAY for what they'd done. Later in the war, the Japanese were decentralizing materiel production by spreading the machines out in their cities instead of putting them in a single factory. So, there might be a shed on your block where there is a machine just making screws all day and night. A couple of blocks over, the machine making the nuts for the screws might be in another shed. You pair that with the heavy use of paper and wood for building materials and you get LeMay's incendiary bombing campaign that effectively met all his goals, military and personal.