The Japanese appeared to have an impressive fleet throughout the war, with ships ranging from:
destroyer classes Fubuki (including the type 2/3 classes, Ayanami and Akatsuki) and Akizuki to the super-destroyer Shimakaze
cruiser classes such as the Takao, Mogami, Tone classes
battleship classes Kongo, Fuso, and the flagship Yamato class
Aircraft carrier classes Soryu, Shokaku, and the more modern Taiho
This surface fleet combined with submarines such as the Type B1 class and the Sentoku I-400 class sounds like an incredibly powerful force on paper - what factors excluding Allied codebreaking and communications interception caused the demise of the Japanese fleet?
Allied codebreaking and other SIGINT ultimately had relatively minor impact compared to the sheer quantitative, qualitative, and technological advantages that the US Navy had over the Japanese one.
The authors of Shattered Sword have a certain webpage in reference to just how massive the Allied advantage was in the Pacific. Simply put, by 1945, the US would have been able to deploy something along the lines of 30 modern CVs, 9 modern CVLs, and over 120 CVEs, against 14 Japanese CVs (of which 1 was arguably even close to the quality level of the US ones), resulting in anywhere from a 2.5 to 3 to 1 disparity in aircraft capability. In addition, the US aircraft were far superior to anything the Japanese could put into the air, and the US could replace their plane and pilot losses, which Japan simply could not due to a combination of poor logistics and a strict naval aviation training regime that made pilot training extremely difficult.
That was just carriers. The US Navy was larger than the rest of the worlds navies, combined. And the US models were the best in the world. In the Battle off Samar, 7 destroyers and a handful of escort carriers, which didn't even have torpedoes for their aircraft, bloodily repulsed a sortie by the main battleline of the Japanese navy, including almost all of their battleships and remaining heavy cruisers.
In addition to Park's spot on answer I wanted to expand on some specific points.
While appearing formidable, the IJN was also an incredibly unbalanced and thus vulnerable force in several key areas.
Lack of effective ASW platform's. Because of the numbers restrictions under the Washington Naval Treaty all IJN ships were heavily focused on offensive potential, and especially her light forces for fighting surface actions. That meant her DD's were particularly poor at ASW, lacking modern weapons and sonar well into the war. Many key ships were lost to US subs which might have had a better chance if protected better.
Lack of effective Damage Control. The IJN viewed DC as a specialized task to be conducted by small cadres of trained engineers and fire fighters, with a few officers highly trained in it from the Engineering Dept and Supply or Maint. Dept. WHile the USN took a much more universal approach making sure every sailor and officer knew something about fighting to save the ships from fire or flood, meaning in general many USN ships took a much greater pounding before sinking or survived what would have sunk an IJN vessel. This disparity grew as the war went on too. Additionally the Type 93 Torpedo was a death trap for any ship that took a hit still carrying them.
Poor IJN Operational planning. the IJN threw away its numbers advantages in the Spring and Summer of 1942 through overly ambitious, convoluted planning that culminated at Coral Sea and Midway. Yamamoto absolutely deserves the blame for allowing and pushing for such a terrible plan. In his drive to sink the USN carriers that had struck back at Japan he became almost oblivious to any flaw in the operation and thus lost his numbers advantage in ships and planes.
Aging ships and technology. While possessing many Battleships, the problem the IJN had was that they were all old. None except the Yamatos had been built following the Naval Treaties, thus they could not fully incorporate new technology and equipment, along with evolving design theory. The Nagato was probably the best BB constructed in the 20's, but with the rise of fast BB's of the South Dakota and North Carolian classes they were once more out of date, while the meat of her battleline was even older. The USN, and RN while still using many older BB's had both begun new construction which would culminate in the best designs of the war. The IJN also suffered from a general lack of AAA on their ships, and was slower to address it than the USN. Those batteries they did have on their Midway carriers for instance were not even able to engage US Dive Bombers until AFTER they had begun to dive!
Meanwhile the IJN was one of the slowest navies to develop and adopt radar, the carriers at Midway lacked even Air Search sets for defense. While the Guadalcanal campaign proved decisively that a training focus on night fighting can still be first equaled, and then bested by a less proficient force adopting radar.