Akai was made to believe, and probably was, smarter than Conan up until the events of Scarlet Showdown.
People assumed the Fake Death plan was a joint plan between Conan and Akai-- turns out it was basically almost all Conan, which was one thing. Same case had Conan being the mastermind behind keeping Okiya's identity hidden from Bourbon. These two things pissed off many people, as prior to this, it appeared that Akai was smarter than Conan. There was a parallel in Kir's intro case, that made it seem that Gin and Akai were equals, right after Gin outsmarted Conan.
Up until Scarlet Showdown, you could of argued that Akai was on par, or superior to Conan. Either we were wrong, or Gosho wanted to nerf Akai to be equal or beneath Conan. The reasons that Akai was made to appear to be above Conan is because Akai's actions, allegiance, and agenda were not known to Conan until Episode 425/Kir Case. Conan figured out that Akai was a myserious character during James Black intro case, and with Ran's exposition, he learned he wore a FBI jacket, but couldn't directly know if he was a real ally or not. Conan and Akai finally work together during Clash of Red and Black. Even during Clash of Red and Black, Akai did not appear to be 'beneath' Conan.