Anticlimax Boss: The final boss in Advance 2 (at least, other than True Area 53's True Final Boss) is the only boss in the game to be stationary rather than a chase battle, which makes it much easier than almost all the other bosses. Parts of the Boss Rush to get to it tend to be more difficult, even!
The best level in the entire Advance trilogy is, by most people's estimation, Music Plant from Advance 2. Its bright, colorful atmosphere plus very memorable mechanics make it a huge favorite among those who play any of the handheld games.
The third game has Chaos Angel, which is very memorable for being one of few final levels in a Sonic game to not be in a factory or space area, instead being floating ruins that are on Angel Island. It is incredibly challenging, has great music, and looks stunning.
Techno Base in Advance 2 is easier than Sky Canyon before it, especially the boss battle. This doesn't mean Techno Base or its boss are easy by any means, but it has a lot less of the instant death.
Advance 3 has Ocean Base Act 3. The first two acts are incredibly long and vertically designed, but the third is a lot shorter, and the only hard parts (getting crushed and drowning in an underwater section) are easily avoided by taking a different path. Twinkle Snow is also easier than Toy Kingdom and Cyber Track, the two levels it's sandwiched between. Other than the boss.
Contested Sequel: The two sequels get this in comparison to the first Advance game. The second game's absolute focus on speed made an exhilarating experience that would later be expanded on by the Rush games, but was also criticized for making the levels feel on-rails and repetitive. The third game is especially criticized for issues like its obstacle and enemy placement bordering on Fake Difficulty and the hub levels being labyrinthe and unnecessary.
Crowning Moment of Awesome: So what if it defies gravity? The ending to Advance 2 is arguably the most badass in the series. To elaborate, if one collects every Chaos Emerald with every character, it opens the secret last zone. Eggman kidnaps Cream's mother, Vanilla, and takes her into space. Sonic goes Super Sonic to rescue her, and he hangs onto the capsule she's trapped in as they plummet back to earth. Sonic loses his super power, the capsule breaks open, and Sonic dives to catch a hold of Vanilla while falling faster as the music intensifies. Of course, Sonic saves her, but the build up is perfect. Sonic saving the world and foiling Eggman's schemes is all well and good, but him saving a little bunny girl's mom from a villain who at that point is just doing it out of petty revenge makes the blue hedgehog feel truly heroic in a very personal way.
Sonic Advance's Egg Rocket/Cosmic Angel can come off as this to some for going overboard with the hazard placement and not being as fun as the levels before it.
Sonic Advance 3's Chaos Angel doesn't apply completely (the first two acts are closer to Best Level Ever), but the third act of it is just standing on moving platforms avoiding obstacles and killing enemies every so often.
Ensemble Darkhorse: Cream the Rabbit. It helps that she is the only character who can defeat the Egg Saucer and the Egg Frog easily while being completely adorable at the same time. Her overly cutesy personality would attract some haters in later games, though.
First Installment Wins: Most consider the first game in the trilogy to be the best, as its level design and general mechanics arguably make it closer to a Sonic 4 than the official Sonic 4.
Game-Breaker: Cream. She can fly anywhere she wants to, and trivializes bosses by sending out Cheese to attack from a distance. Tails and Knuckles are too, to a lesser extent, as since the levels are primarily designed for Sonic, their flight and gliding trivializes all platforming.
Some of the character combinations in the third game can be this.
Note Sonic with Cream, where Sonic can not only get a fair bit of height, and use Cheese to attack enemies, but also breathe underwater, without a major sacrifice to his innate abilities that you would expect as some combinations often neuter one character.
Knuckles with Tails gives not only Tails' height skills, but Knuckles can double jump before gliding, making this pair very good for exploration. (The other way around is nowhere near as effective, due to Tails clumsily imitating Knuckles' gliding.)
Knuckles and Amy is basically the same, only replace the double jump with the insane ability to spin dash up walls.
Tails with Amy improves Tails' flying speed and height drastically, and allows him to use a hammer while flying. The hammer has a much larger attack radius in midair, rendering most of the levels extremely easy.
Guide Dang It!: R button tricks, which are necessary in the second game in order to beat Sky Canyon, unless you're using a flight character. As it was a new mechanic to the series, it often took a while for many players to realize what they were doing wrong. These are in the manual though.
To get to the Special Stage in 2 to even attempt to get a Chaos Emerald, you had to collect all 7 of the Special Rings hidden through a level. Unfortunately, as a later Sonic game, it wasn't really known for its exploration and most players would end up running right past them (especially likely given the game's emphasis on seed). It doesn't help that backtracking is pretty much impossible and players would either have to memorize an entire level to get them or get the game guide with the detailed maps. And you lose the rings you got if you die. Also, think you can use Tails to fly around and open the way for the secret level more easily? Nope, the emeralds are not shared between characters. And the Special stages themselves are nigh-impossible.
Rescued from the Scrappy Heap: For those who didn't like Amy's much slower style of play in Adventure, Sonic Advance had a lot of people warm up to her thanks to her playstyle in that game, thanks to it still being fairly speedy yet still incorporating her unique moves.
Sonic Advance removed the Insta-Shield's invincibility, which was the entire point of the move. Advance 2 then rendered it even more useless with its level design direction and the fact it is overriden by the Homing Attack most of the time.
Getting the Chaos Emeralds is a large pain across all three games in some way. In the first game, it's the Special Stages themselves being awkward to do, in the second game it's having to collect the Special Rings in order to access the Special Stages, and in the third game it's having to scour levels for Chao.
Also from the first game, the first half of the Neo Green Hill Zone themes sounds hilariously similar to the refrain of "Edelweiss" from The Sound of Music. (The melodies do eventually diverge, though.)
Tier-Induced Scrappy: Surprisingly, Sonic himself gets this in these games, but especially the third one. He doesn't have any truly unique abilities like the others, and the levels are really designed to take advantage of the other characters' abilities, and Sonic's ability to grind rails note exclusive to him and Amy in the first game; the later ones gave it to Knuckles, Tails, and Cream as well feels mostly tacked on. Choosing Sonic can actually make Advance 3harder to play.
Ice Mountain in the first game, especially as Sonic. As an Underwater Boss Battle with a high level of water, drowning is always a risk and jumping on the falling stalactites to make it to the surface is tricky. It's easy with Tails, Knuckles or Amy, but not so much with Sonic.
The boss of Sky Canyon in the second game, who is the only boss in the trilogy with a One-Hit KO attack. And yes, you have to fight it again in the Boss Rush. It also has a unique boss theme, and it's rather creepy-sounding note that track only plays during the first half of Sonic's encounter with the machine [known as the Egg Saucer], when Knuckles is in the cockpit, since it switches to the "pinch" theme after four hits; all other times Eggman will be in the cockpit and the normal boss theme plays
The boss of Twinkle Snow in the third one, where you have to ascend platforms that fall when you touch them and get them to hit Eggman. He also has a mace which knocks you into the Bottomless Pit below if it gets you. Also, the mace can knock down platforms too, which screws you over if that was the one you were about to jump to. Basically, this boss functionally has only a One-Hit KO, can't be hit directly or by Cheese, and it doesn't matter if you can fly or not. This is one of the bosses where Amy shines at because of her awesome high jump ability.
The boss of Toy Kingdom in the third game can be somewhat irritating, as the boss spawns enemies that can be annoying to defeat if Amy is involved, and the Gemerl bomb can be hard to dodge and can easily knock you into the inescapable pit. It generally becomes easier as the fight continues, though, as the arena space increases.
That One Level: The last special stages in the first and third games have a ridiculous difficulty spike from the sixth stages. Fortunately, retrying them isn't that hard, but you can still expect to spend at least an hour retrying them.
Egg Rocket in the first game can be a pain no matter who you're playing as, especially as Sonic or Amy, as the zone is quite confusing to navigate, laden with bottomless pits and annoying enemy placement, and has fewer and farther-apart checkpoints than the other zones in the game. It's also timed when you enter the rocket; there are three sections with their own timer, and being left behind in one when the clock hits zero will see you get detached from the Egg Rocket and take a life.
Sky Canyon in the second game can be a pain too with Sonic, as it's just as pitfall heavy as Egg Rocket. And if you don't know about R Button Tricks, you won't be able to beat it. And once you get to the boss, you have to hope it doesn't pull its One-Hit KO.
The later zones in the third game, particularly Cyber Track and Chaos Angel, can be pretty damn evil with bottomless pits that are as frequent as the above examples and the level design. In fact, 90% of Chaos Angel Act 3 is a moving platform ride across a colossal pit with a lot of enemies, spikes and other things that will knock you off!
What An Idiot: Knuckles gets tricked by Eggman into fighting Sonic for the third time. Even Sonic was annoyed about this after the boss battle.