His claim to genius rests on one masterpiece: Pearl Harbor.
On the "just lucky" side of the ledger, we have some serious failures.
1. He completely misread his opponent. He dismissed the US Navy as “a social organization of golfers and bridge players.” He expected the shock of Pearl Harbor to bring the US to the negotiating table. Failing that, he counted on his initial onslaught to buy Japan 12-18 months of US inaction that would let her solidify her gains.
The much-maligned Adm. Nagumo was much more astute. He argued against the Pearl Harbor raid precisely because it would preclude the negotiated settlement that was Japan’s best hope. No matter how brilliant it was operationally, it represented a grave strategic error.
The operational success also produced smaller short-term gains than Yamamoto promised. Defeat at Pearl Harbor did not paralyze the US Navy for 18 or even 12 months. Nimitz’s forces were conducting carrier raids against Japanese bases by February 1942.
The first, the supreme, the most far-reaching act of judgment that the statesman and commander have to make is to establish … the kind of war on which they are embarking; neither mistaking it for, nor trying to turn it into, something that is alien to its nature. This is the first of all strategic questions and the most comprehensive.
Clausewitz, On War
2. Like many Japanese officers he was quick to believe that his enemies would act as he needed them to act for his plans to work. Hence, Midway.
3. He showed no real skill in the improvised war of 1942-1943.
Too much of the Japanese plan hinged on its flawless execution and too little margin for error was left to absorb the unexpected friction. While it is possible though inadvisable to to make such assumptions in the opening phase of a war against an unsuspecting victim (as in the case of Pearl Harbor), it is practically suicidal to assume that any complex plan can be executed perfectly in an ongoing war.
Michael Handel, Intelligence and Military Operations
4. He had no sense of what Clausewitz called “the culminating point of victory.” Japan’s grand strategy called for victory through determined, protracted defensive warfare to force the US to accept a compromise peace. Yamamoto never really turned his mind to preparations for this phase of the war. He looked always for fresh opportunities for conquest: Midway, the Solomons, New Caledonia, Ceylon…
"One cannot ignore the simple fact that not a single [Japanese] operation planned after the start of the war met with success
H. P. Willmott, Empires in the Balance
These hopeless adventures and impossible fantasies squandered irreplaceable forces and delayed preparations for the defensive struggle that would decide Japan’s fate and even her survival.
Japan reached its level of incompetence, where it fought with all its power and to the death. The battlefields of New Guinea and the Solomon Islands were simply too large and too far forward to suit its tiny logistical and transport capabilities....Japan was fighting precisely the war which least suited its material resources, a prolonged and costly battle of attrition beyond easy reach of its supply system.
Michael Handel and John Ferris, "Clausewitz, Intelligence Uncertainty and the Art of Command”
5. Japan launched the war to acquire vital raw materials. Yamamoto, who served as Deputy Navy Minister before he took command of the Combined Fleet, never developed a doctrine, a strategy, nor the forces necessary to protect the sea-lanes that carried those resources to the Home Islands. This failure left Japan practically helpless against US submarines. From 1943 onward, the Japanese war machine was slowly strangled even as her admirals dreamed of the “decisive battle” that would win the war in a day.