Jak suddenly wanting to return to Haven City. He was given the perfect opportunity to go straight back there thanks to Ashelin, but rejects it and angrily says that he's staying in the Wasteland. Then suddenly the game points you in the direction of the temple to get him back home with no transition whatsoever, nor any scene building up to this.
Ashelin suddenly having enough power and authority to dissolve the city council on a whim near the end of the game when in the beginning she couldn't even stop them from banishing Jak. To be fair, by that point, Jak no longer had a 0% Approval Rating, and the council itself had enough of Veger.
Big-Lipped Alligator Moment: There's a mission where Daxter gets sucked into a computer and has to play a Pac-Man style game to find a MacGuffin. It evidently wasn't supposed to be that much of a stretch, since the character who put him into the computer was one with the computer himself, but Daxter's whole body getting sucked through the screen?
Contested Sequel: Downplayed; fans are divided on whether this is the best game in the trilogy, the weakest, or even the middle, but those in the "weakest" camp still generally regard it as a good game in its own right, and a good ending to the trilogy nonetheless.
Fanon Discontinuity: Downplayed example. The game isn't seen as Sequelitis, but fans refuse to treat the cutscene where Jak coldly refuses Ashelin's offer to return to Haven City as canon, opting to skip it and pretend it was Ashelin who refuses to take Jak back.
Game-Breaker: The Beam Reflexor upgrade for the Blaster. The shots bounce off walls and home in on enemies and it can be fired fairly frequently, allowing it to easily clear even very large rooms in under a minute. It's also one of the very first upgrades you get in the game. Using the "jump-spin-fire" move usually destroys anything on your way.
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.
Light Jak's regeneration invokes this with a high-pitched crystaline humming noise as your health fills back up.
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 Mechanic: The Titan suit again, though this time at least it only has one mission.
Strangled by the Red String: Another downplayed example. This game gives a few ship teasing between Jak and Ashelin, but downplays Keira's role, leading fans to assume that the first two are in a relationship. It doesn't help that there's an implied kiss at the end between them, and to be fair, the second game also had moments between them. As a result, Keira was given a larger role in the next games to fix this (although The Lost Frontier wasn't well received by fans) .
Underused Game Mechanic: One new feature that many fans felt was disappointing was the implementation of Jak's new Dark Eco ability of Invisibility. Aside from an once-visited volcano level, it could only be used at the Monk's Precursor Temple monastery, thus meaning any use of it this for any stealth based tactics (or for that matter any sort of stealth-based missions) outside that location is denied to players. Granted while there is an unlockable ability to turn invisible by pressing the triangle button in Dark Jak form, but that only becomes available after completing the game (though it is somewhat subverted if someone buys it from the Secrets menu and then starts a New Game on Hero Mode).
During the sections that you play as Daxter, it is possible to kick while hanging from ceiling grates. Since there are no enemies or breakable objects up there, this is never put to any kind of use.