Anti-Climax Boss: Gnasty Gnorc. His attacks will only hit the Spyro if he's standing still and after the key to lower the platform on is grabbed from a thief, the rest of the fight is spent chasing him with almost no real resistance.
That One Level: Tree Tops. It's a relatively short level. As if. It's very easy to fall off (being a Floating Continent-type level), has some mildly annoying enemies (the large ones have a somewhat wide-range kick, and the smaller ones throw banana bunch-like projectiles without any sound cues), and to get everything, you're gonna need to pull off some Guide Dang It-y Super Charge maneuvers. Route is outlined here. Spyro even Lampshades this by complaining to the dragon that he "could have found an easier spot to get stuck."
Haunted Towers, where a supercharge through several metal doors leads to a room filled with more metal doors (you must run back up several times to re-Supercharge down into another door to open them all, or look up which door the fairy is behind and use the resulting superflame). One leads to a pool area with a ramp, implying there is some mythical way to Supercharge down the path, take a right, and somehow charge around the extremely narrow ramp and then jump to reach a hidden wall where a trapped Dragon and treasures are hidden. Said mythical way involves supercharging into the pool area, veering left (the ramp in that area is to fake you out!) and leaping off, landing on the next section which is an area you've already been in just getting to the supercharge, charging up that ramp, then leaping onto a hidden platform with a whirlwind. Guide Dang It! See it here. At least it's easier than Tree Tops.