Banjo-Tooie has become somewhat infamous for its large-scaled and convoluted structure in comparison to its predecessor, Banjo-Kazooie, with far more larger interconnected worlds with longer, complex puzzles that typically require backtracking, in comparison to Banjo-Kazooie's more straightforward and compact, self-contained levels and objectives.

According to Steve Malpass, one of Banjo-Tooie's game designers, the game was designed more in the vein of an adventure game as opposed to a platformer, being heavily inspired by The Legend of Zelda: Ocarina of Time in particular. The development team was aware of how overcomplicated the game's structure had become by its launch (the QA department was vocal about the backtracking and navigation issues), but it was ultimately too late for them to streamline it. The Warp Pads found throughout the worlds were actually included after the levels were designed, as an attempt to mitigate the aforementioned navigation issues.