These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Anti-Climax Boss: Metal Overlord. While Metal Madness is mildly challenging due to having one instant-kill attack, Overlord is one of the easiest bosses in the game—you can't even be directly harmed by him, and the only danger is running out of rings, which can be periodically refilled during the fight.
Broken Base: The game itself caused a sizable rift in the fandom. Depending on whom you ask, it's either a fun and engaging platformer with a nice variety of characters and the last good game before the franchise's Dork Age, or an unplayable mess with awful controls and the very game that started the Dork Age.
Best Level Ever: Many players hold Egg Fleet as the favorite, not only for the sheer sense of vertigo of being high up in the air (even compared to other airship levels in the series), but for the challenge offered by having to constantly dodge gunfire from the ships, and the sheer amount of alternate paths available. To put the cherry on top, the level features the playable trio creating a chain reaction that destroys an entire battleship with Rocket Accel. And Team Sonic's version allows you to do it three times, with the third time standing in for the Goal Ring. Quite expectedly, there are a number of fans who are disappointed that Seaside Hill, essentially the Green Hill Zone throwback of the game, was picked to represent Heroes in Sonic Generations over Egg Fleet when, one, theGreen Hill Zone was already in the game, and two, Seaside Hill had already made countless appearances in many spin-offs.
Character Rerailment: The SonicAdventure series turned Knuckles into a dead-serious guardian, in sharp contrast to what the artwork for the first game showed, and to his Sonic 3 & Knuckles portrayal of laughing at Sonic at every turn. This game was able to reconcile the two portrayals into a deceptively stoic yet laid-back Lancer who gets smug at getting one over Sonic.
Team Chaotix has the least role in the story, but are far more popular than most of the other teams storywise (gameplay-wise, however, their "search mission" gameplay tends to be near-universally despised).
E-123 Omega is pretty popular as well, both for his amazing power and his awesome (though somewhat hammy) quotes.
Metal Sonic copies Chaos's data from Chocola and Froggy. Chao are very closely connected with Chaos, and Froggy was once possessed by Chaos. When Metal Sonic enters his One-Winged Angel transformation, he does so by merging with one of Eggman's battleships. This is because he copied Chaos's shapeshifting powers. However, while Chaos is made of water, and thus merged with Station Square's reservoirs, Metal Sonic is made of metal, so he used a battleship to gain mass.
Goddamned Bats: In the Hang Castle and Mystic Mansion stages, the ghosts that pop up everywhere.
Egg Bishops/Egg Sorcerers, one enemy with two different forms distinguishable by color. Egg Bishops (orange) have the ability to heal themselves and any enemy nearby. Egg Sorcerers (purple) can cast a spell that steals all your rings. And the worst part is if you use a tornado attack on them, it just flips them over to the opposite form, making a bad situation potentially even worse.
Harsher in Hindsight: In this game, Metal Sonic ends up backstabbing Eggman and trying to defeat Sonic himself by gaining more abilities with implied modifications. Three years later out-of-universe, Metal Sonic does it again in Super Mario Bros. Z, only it ends up being far worse than before, where he (presumably) murdered Eggman while backstabbing him, demolished a large percentage of the planet's ecosystem, and also murdered all of Sonic and Shadow's friends.
It Was His Sled: Metal Sonic was the real villain of the game, while Eggman was locked up the whole time. The trailers didn't even try to hide that Metal was making a comeback. His trophy description in the fourth Super Smash Bros. doesn't help.
Mondegreen: Several gamers thought that Knuckles said "Shit!" during the first of his combo punches.
"Take this! Take this! Take this! Take this! Take this! Take this! CHARGE!!!"
Anyone who is the point man when you go into the cannon in Bullet Station. The team is shot out of the cannon and can pick up item balloons as they go through the air, subjecting the player to the snippet they say over and over.
Rails, which began to be overused and often have Bottomless Pits under them. This game was also the first in the series to have the characters talk about the scenery and their current situations, a source of many annoying sounds, Captain Obvious statements, and Narm, which people often complained about.
When hit by an enemy, a character gets stunned for a second, giving you less time than usual to collect your rings before getting hit again.
Enemies having life bars were a constant early complaint, since they messed up the flow of the game (especially if your characters weren't leveled, which meant that only Power-type characters could reduce their HP without additional effort, and later enemies carried HUGE life bars AND barred progress until defeat), and turned parts of the game into a crude Beat 'em Up instead of a traditional speed-based puzzle/platformer.
Flying formation can be a pain, as you're forced to carry your teammates and speed is reduced greatly is this formation. And if your fly meter depletes fully, you sink like a rock, which can be frustrating if there's a Bottomless Pit below you, which is to say, quite often in fly specific areas. Also, there's an inexplicable height cap when you attempt to fly that is all too easy to reach, which really ruins the point of a "Flight" formation. Attacking in flight formation can also be rather tricky, as it can be hard to aim.
Special Effect Failure: The CGI in the cutscenes was low budget and generally mediocre, even for the time of its release. It's tolerable for most of the game, but the ending cutscene really takes a nosedive in quality in compared to the others—one glaring failure is Rouge floating across the ground when she's clearly supposed to be walking in the ending cutscenes (her body moves before the legs do, which makes it look like she's skating on ice).
In the cutscene where Team Rose were tricked by an Eggman decoy, Big sadly utters out "Froggy, where are you? Let's go home." You have to feel sorry for him since it looks as though he's failed to rescue Froggy and he's given up in doing so in the process.
The Team Dark scene where Shadow spots a Shadow android, which gives him the thought that he may be an android as well. The shot where Rouge sympathetically looks at Shadow really tells the story.
Final Fortress, for its multitude of mandatory enemy gauntlets involving the strongest enemies in the game.
Mystic Mansion, which is also a Marathon Level. Bonus points for Team Sonic's final room especially, where you have to cross all three gaps with the different mechanics.
The Special Stages, too, especially where you have to catch the flying emerald. Doubly so as Team Rose, which is a little bit slower than the other teams.
Rail Canyon and its following level, Bullet Station, for consisting of little more but rail grinding and virtually zero safe ground below you.
They Changed It, Now It Sucks: Some people are not fond of the designs for Tails' and Knuckles' Super Mode (more akin to a "Super Shield" than their actual transformations from S3&K) in this game.
Tough Act to Follow: Since this game followed the immensely well-loved Sonic Adventure 2 (both the original Dreamcast version and its GameCube Battle port), Heroes did, and still does to this day, get a lot of bile from fans for really slippery controls and its utter repetitive structure compared to Adventure 2.
The Untwist: There wasn't really any effort to hide the fact that Metal Sonic is the real villain; he makes several, albeit brief appearances throughout the game, including the opening cutscene. Yet when he finally introduces himself, it's still treated as a shocking revelation.
Visual Effects of Awesome: Metal Sonic's One-Winged Angel, which involves a fast-paced sequence of parts of a blown apart tower assembling together into his new Metal Madness form, with Metal's head morphing into some... thing that completes his transformation, all lasting for circa 50 seconds.