Even Better Sequel: When compared to the previous game, and for that matter, any of the games between Up Your Arsenal and this one. Not only it improves on the gameplay of it's predecessor Tools of Destruction, but it introduces several new features like the ability to travel around the space with the spaceship as opposed to a Point-and-Click Map like other games, as well as having two kinds of gameplay between Ratchet and Clank, great level design, more creative weapons, more boss fights, and the return of Dr. Nefarious as the Big Bad, the result is a game that is widely seen as the best of the Future sub-series. It's been so acclaimed that, if there's one game that easily reaches (if not surpass) the quality of Up Your Arsenal as the best game in the franchise, it would be this one.
Fridge Logic: In the Recap cinematic, Captain Qwark stated his reason for not being present in Quest For Booty, and that was for shooting for a new holo-film. However, Captain Slag and Rusty Pete both had parts in the film as well, and they both had significant roles in QFB. How could they manage the time to film alongside Qwark as well?
Solution: Qwark was also filming Unicop in-between the two games. It might have been filmed first, while My Blaster Runs Hot was filmed afterwards. This would make sense, considering the amount of time and costs it would take to finish Unicop because Qwark plays a unicorn in the film, while he's just playing himself in My Blaster Runs Hot, so there's a good reason who the latter was released, first.
Harsher in Hindsight: After you've seen Azimuth go nuts and kill Ratchet in his quest to rewind time, his unceasing ranting throughout the game suddenly sounds much more unhinged than it did on your first playthrough.
Moral Event Horizon: Alister Azimuth kills Ratchet at the end of the game. Shortly afterward, he becomes the final boss and nearly destroys the entire universe. However, since Ratchet's death is undone by Clank and Alister finally sees the error of his ways, sacrificing himself to prevent the destruction of the universe he almost brought upon it, fans generally don't consider him too far-gone to be denied posthumous redemption.
"Unnecessary Initiative Omega 91" is this for Cassiopeia, given she spends the entire time trying to kill Ratchet and orders the other Valkyries to execute Clank. And like Courtney Gears before her, Cassiopeia is quite sadistic over this.
That One Level: Krell Canyon has a part during the first stage where Ratchet must move two platforms over a bottomless pit to bypass a tetromite nest. Unfortunately, it is very possible for the tetromites to reach the other side and wait for Ratchet to leap over to them, making it almost impossible to reach water before his HP reaches zero.