Diving a little into the Japanese planning and execution ...
The attack routes for the most potent attack planes, the torpedo bombers were complicated and pretty much guaranteed plane-plane interference.
The attack routes for Battleship Row did not take into account what some of the routes would fly over (structures with different heat effects) and how the turbulence would complicate an already difficult to achieve altitude and speed necessary for a successful torpedo release.
There was no "Plan B" for torpedo planes assigned to attack carriers, which would be moored on the other side of Ford Island from Battleship Row, other than find a worthwhile target. The net effect was that many of these planes went after the battleships, causing confusion in the line-up of planes already attacking Battleship Row.
Individual torpedo planes were not assigned specific targets. Pilots were expected to select targets, planes later in the string being expected to select and attack undamaged ships. Aside from the capsized Oklahoma, torpedo damage was well below the waterline, not easily discernible to pilots who had seconds in which to pick a target, achieve proper altitude and speed, and drop their torpedo. The net effect was that most pilots took a relatively easy route (making those later in the stream nicely spaced targets for AA) for which the easiest targets were Oklahoma and West Virginia, resulting in those two ships being hit by more torpedoes than "necessary" (WeeVee was hit by 7 torpedoes; she sank, but due to good damage control did not capsize) while other battleships were only hit by one or two.
Due to the narrow speed-altitude window in which the torpedoes cold be successfully launched, the very brief time to achieve it, and significant harassment from American AA, some torpedoes ended up only hitting Pearl Harbor mud.
A portion of the torpedo bombers carried armor-piercing bombs - re-machined and adapted 16.1" shells (used by Nagato and Mutsu) - to attack the battleships torpedoes could not reach. There was one spectacular success, Arizona, but there were many misses, and some hits were duds or partial duds. Apparently the re-machining weakened the shell cases enough that some broke open, spilling the explosive filler which then could not be exploded by the fuse.
First wave dive bombers were assigned various airfields. While the purpose was to prevent land-based counter-attacks, the effort expended was excessive. Some should instead have been assigned to attack cruisers and destroyers. Neither the first-wave nor the second-wave dive bombers carried armor-piercing bombs. The bombs they carried were general purpose, with a .2 second fuse delay, optimized for ships with unarmored decks (the bombs would penetrate into the ship before exploding).
Second wave bombers were assigned to attack less damaged and undamaged ships. The pilots tended to go after battleships, especially the Nevada, but other than damaging superstructure, their bombs could not sink a battleship. These dive bombers should have specifically been assigned to attack cruisers and destroyers (which some did).
Fighters were not assigned to escort torpedo, horizontal, or dive bombers. Their assignment was to take out any US fighters found in the air at the start of the attack, and then to strafe planes caught on the ground. Strafing, instead, AA on ships could have saved several torpedo planes and crew who were shot down. While this did put Oahu out of operation as an airbase this was very temporary. And since many destroyed plane were obsolescent or down-rev, the replacement planes were current types and Oahu was at greater strength within a few weeks.
Each wave's attack routes and assignments were very complicated, and would have benefited from flexibility and some kind of traffic controller who could observe and direct planes against under-attacked targets. IJN plane radios were poor, installed in places making them difficult to use, and pilots who had voice radio found the quality so poor that they would not bother to try to use them (this problem continued to plague IJN planes into the Solomon campaign, at least). Thus, there was no attempt to have a coordinating observer.
The attack plans had a list of targets, by priority. Contrary to Fuchida's ... falsehood ... fable ... lie ... (you pick), an attack on the naval facilities and oil storage was never considered. At all. Those facilities were at the very bottom of the priorities list. The surviving planes that could hypothetically have done a third wave could not have made a dent in the vast naval facilities at PH. And if instead they focused on the fuel storage, they could have done significant damage, but not wiped out the storage. The USN would still have had significant amounts of fuel untouched, and rebuilding the tanks and filling them would have been a matter of a month or two. Secret, at the time, the USN also had a hidden underground storage facility, some of which was ready or almost ready to use.
Japanese planning, execution, and bomb quality were seriously flawed. They did significant damage, but far from what they could have, even with the IJN's poor radio technology.