Broken Base: The over focus on other characters instead of Spyro himself. About half the game is spent controlling Spyro while the other half is spent controlling other characters with many, many different playstyles. Some feel it was a good way to spice things up, while others felt it took away from the game, to the point some claim Spyro was mostly there to get you to buy the game in the first place. (The fact that Gameplay Roulette fell out of style near the mid-PlayStation 2 era doesn't exactly help either...)
Breather Boss: The Giant Stingray is That One Boss for Sparx. Scorch is a fine boss by himself but he comes after a Spike, the toughest fight in the series save Finals, so the devs decided to throw you a bone. The missiles Bently throw to you lock in on Scorch so easily that you almost have to try to miss. The battle format also allows you to hit him every time that he attacks, which is often, and Bently throws more healing items than normal as aposed to Spike's battle where S. Bird rarely, if ever, throws any healing items.
Catharsis Factor: One of the first things you can do post-game is chase down Moneybags and kick the ever loving crap out of him in order to get back the gems you've spent over the course of the game.
Contested Sequel: Some feel like it's the best of the original trilogy, managing to build on the set formula from the first two games. Others feel it's the weakest of the trilogy, for the above reasons stated in Broken Base. And others feel that it's better than the first game, but not as good as the second one.
Game-Breaking Bug: Flaming Fluffy, the cat-shaped fairy that gives the egg to Spyro upon completing Cloud Spires, at the same time he (or she) speaks with you will not trigger the cutscene. Speak with Fluffy again, and he'll act like the cutscene has played, but will not give out the egg and just disappear into an invisible portal. This will trick the game into thinking that the realm has not been completed. Entering and exiting the sub-level with the sun seeds will bring Fluffy back, but he cannot be spoken to. The only way to complete the realm is to exit and reenter Cloud Spires.
The Sorceress' boss battle on the original NTSC version. Due to a glitch, your final battle is being conducted to the tune of Sunrise Spring. The battle was SUPPOSED to have it's own theme as it is present in the disc, though this was fixed in the Greatest Hits version. Both PAL versions also use an incorrect tune, though the more fitting Spike boss theme.
While Bianca's arc is poignant, it's somewhat hindered by her especially limited 3D model and perpetual Smug Smiler facial expression.
Scrappy Mechanic: Downplayed. While no one hates the characters specifically, a few of the partners aren't looked upon favorably thanks to their levels resembling a slower paced, less interesting version of an existing character's level. The prime offenders tend to be Sheila note which gets compared to Spyro's own gameplay, Bentley note which, again, gets compared to Spyro's own gameplay, and somehow manages to be far more clunkier than Sheila's, and Srg. Byrd. note thanks to his flight being a clunkier version of Spyro's own, which could have been easily expanded upon.
Ship Tease: Between Spyro and Elora during the ending (although only on Elora's side). She asks him if he's going to visit her any time soon and tells him to enjoy the fireworks show (with her) while Bianca and Hunter are kissing.
Talking to Himself: Neil Ross voices both Moneybags the Bear and Bentley the Yeti. Which makes the scene between them also a case of "beat the crap out of yourself with a giant club."
That One Boss: Spike. He's similar to Ripto, attacking with energy balls that are ridiculously hard to dodge consistently and, in the second and third phases, can take the powerups for himself. In addition, the first phase requires incredible precision and speed to the point where you will likely get hit, and the latter two phases, while easier, are still a challenge.
That One Sidequest: Any of them can count but the most infamous is the Escort Mission where you have to protect Nancy from Rhynoc Hockey Players all while the most annoying song (or pleasurable if you're a sadist) in the game plays. Expect to die many times before succeeding and having That's OK ingrained into your skull.
All of Agent 9's missions can be really challenging. The First-Person Shooter mission in Fireworks Factory is probably the most infamous, where you have to go through a number of rooms while shooting down many ninjas with your laser gun, which fires too slow in this situation. There can be a lot of ninjas in one room and it can be hard to take them all down, especially when they keep respawning via Mook Maker. To add to that are the wonky controls which are not programmed for a first-person shooter. And that's not all; after you retrieve the egg, Handel is in trouble and you'll have to go back and save him... by going through the hordes of ninjas once more. To make this easier, you can get a hidden weapon (which is also a Skill Point) which fires more rapidly, but eventually you'll run out of ammo and go back to using the laser gun.
Another annoying Agent 9 mission is done in an automated Rail Shooter, and you would have to clear out some dinosaurs. The problem with this is that the mission can take a while to get done and the later half can be exceptionally brutal with the number of dinosaurs on-screen.
And finally there's the Haunted Tomb mission where Agent 9 is shown in an overhead view, and what happens is that the player gets trapped in one of 5 arenas that you'll have to go through, while being cornered by tons of enemies. The more you advance the more enemies that appear, and they range from 20 or so cobras who try and Zerg Rush you to large enemies that you'll need to use their own weapons against them in order to destroy them. Thankfully, there is a glitch that lets the player skip all of this.
What Do You Mean, It's Not Symbolic?: In Evening Lake, there is a whale swimming in the deeper regions of the lake. If you swim up to its mouth, the whale will eat you, revealing a dragon egg inside its stomach. The dragon inside the egg is called "Jonah." On the other hand, a lot of these dragons have joke names.
They Wasted a Perfectly Good Character: Bianca is a major supporting character throughout the game, eventually making a Heel–Face Turn just before Spyro reaches the final world. Despite being built up as the perfect character to become Spyro's final playable ally against the Sorceress, she remains an NPC and the game instead introduces Agent 9 as the last playable character to free. As a fledgling sorceress, Bianca would have had just as much room to be an interesting playable character, and was much more relevant to the story.