Harsher in Hindsight: One of the adverts for the game parodied Luke, I Am Your Father, with Daxter attempting to convince Jak he was his father and the announcer assuring the audience that the game wouldn't "end like this". He's right. In the game proper, Jak does meet his father, but it ends tragically, with Damas dying before he would ever know that Jak was his son.
Moral Event Horizon: When exactly Count Veger crossed it is up for debate, but it's widely accepted that he crossed it. Many point to his gloating to Jak immediately after Damas' death as one.
Narm: The battles between the Freedom League and the Metal Heads/KG bots become hard to take seriously, especially after the War Factory is destroyed. The entire city sans the port consists of endlessly respawning soldiers and enemies killing each other over and over. You can't even help effectively because the FL troops are just Palette Swaps of the original guards, so your weapons will automatically target them too.
Scrappy Level: The Nintendo HardPac-Man esque minigame in the power station. It becomes a lot easier though once you realize that you can speed up Daxter's movement.
Shocking Swerve: There are quite a few in this game such as the Precursors actually being ottsels like Daxter with highly advanced technology or Jak actually being Mar.
Strangled by the Red String: This game has Jak and Ashelin become a couple, despite the previous entries of the series has Keira and Torn as Jak's and Ashelin's respective love interests. Jak X and The Lost Frontier would ignore this and restore Jak and Keira's relationship.