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...)
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 throws 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.
The Rhynoc Wizard of Spooky Swamp is pathetically easy, with a fighting strategy consisting solely of summoning the small gators you've been beating throughout the entire level and throwing a Cartoon Bomb that can easily be headbutted back. In comparison, the Robot Shark of Seashell Shore (the previous Mini-Boss) is far tougher.
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.
Demonic Spiders: The gun-toting T-Rexes in Dino Mines will absolutely murder you if you don't murder them first, as their shots are surprisingly accurate and dodging at close to mid-range is almost impossible. The dynamite-tossing ones are just as bad too, due to them aiming their explosives to where Spyro will go instead of his current position.
Goddamned Boss: The Chinese Dragons of Fireworks Factory are not exactly tough, but they're still annoying to handle due to them being very fast and slim, making them hard to hit with your fireballs.
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 its 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.
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 Level: Dino Mines is well-justified in being the final level before the Final Boss. It features some of the game's toughest enemies as well as two of the game's hardest side-missions (an Agent 9 Rail Shooter described below and a fast-paced underwater tunnel segment where you cannot get hit once, which becomes ridiculous once you see the amount of explosive crates floating around at the tunnel's very end).
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, this time in Dino Mines, is done in an automated Rail Shooter and it's about clearing out some dinosaurs. These said dinosaurs are a pain to get rid of; sniping three or four of them on-screen requires you to be sharp-witted with perfect accuracy on top of it. If not, prepare to be constantly shot at. Health restoration is also missing (besides a Skill Point dino being available halfway, but the player would have to be extremely quick otherwise it's a lost chance) so you can only take about four or five hits before going down, and it doesn't help with this mission taking a while to complete.
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.
The slide in Crystal Islands, which is relatively simple in terms of the later sidequests in the game but the fact that you can lose lives just by falling makes it a lot more dangerous. There's also the matter of Spyro's slippery controls on the slide being a combination with the tight turns you'll have to manuveur and there's also gems (which you might miss and have to return to the beginning to get) along the way to add to frustration.
Haunted Tomb also has the tank battle minigame, where you have to blast some tank-riding Rhynocs with your own. The first round is reasonably fair, but the championship round is almost impossible to do normally due to the tank being very slow and 3 or 4 Rhynocs constantly ganging up on you. It's possible to snipe half of them away, but it requires patience and only works for the last remaining ones which are away from the central arena.
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.