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.
Anticlimax Boss/Disappointing Last Level: Gamma's second phase, defeatable with just a single Top Spin. By extension, Dr. Wily's castle as a whole could be considered to be one big anticlimax, considering the Wily stages are arguably much easier than the Doc Robot levels. It is very dry of enemies and dangerous platforming, not to mention they litter the place with e-tanks and extra lives.
Fanon: Some hardcore fans like to assume that Dr. Wily actually died in the collapse of Wily Castle, considering 3 the final "true" game of the Mega Man Classic series, and ignoring everything from Mega Man 4 and beyond.
Game Breaker: The Rush Jet is ludicrously useful in this game, making a platform that can move in any direction and only uses energy when Mega Man's feet are touching it. With a trick, you can get it as early as the second stage. It gets severely nerfed in subsequent games.
It does become somewhat of a necessity, however, as the energy pellets collected to fuel the jet across wide gaps (such as in Needle man Revisited) are not restored if you lose a life.
Scrappy Mechanic: While not that bad of a weapon overall, there can only be one shot from the Gemini Laser on-screen at any one time. If it misses, you can't fire another shot or even pause the game until the shot either leaves the screen, runs out of energy or hits an enemy, which is doubly problematic if you're fighting a boss and low on energy, since it'll temporarily prevent you from using any energy tanks that you have.
Scrappy Weapon: While Top Spin can be used properly in boss weapon-only runs, Spark Shock is possibly even less useful than said weapon. Unlike Ice Slasher, you can't switch to another weapon to lay on the hurt on the paralyzed enemy, or freeze another enemy while the current shot's on the screen.
That One Boss: Needle Man and Shadow Man, if you don't have the right weapons.
Needle Man erratically jumps around, spamming the Needle Cannon whenever he feels like. Sometimes he'll ignore physics, land in front of you and try to impale you with his needle head. Twitch reflexes are your only hope.
Shadow Man is a Bullfight Boss. On every third jump he will either fire the Shadow Blade (slide under this) or he will immediately slide towards you and then cancel it into a jump when he's right in front of you (properly jump your jump over him). Basically you can beat him as long as you back away and give yourself enough time to twitch away when he does something, and control your distance.
It doesn't help that Shadow Man's weakness is the Top Spin: you have to be CLOSE to hit him.
A few of the Doc Robot battles. Namely, Quickman; while he was a Fragile Speedster in Mega Man 2, Doc Robot Quickman is a Lightning Bruiser, able to not only deal a lot of Collision Damage, but his larger size makes him much harder to avoid. This is also an issue with Doc Robot Flashman; due to the fact that you fight him on stairs, he's very difficult to jump over as a result.
There's also the larger, harder-hitting Wood Man Doc Robot (whose size also makes his Leaf Shield bigger), and the Air Man one which throws tornadoes in undodgeable patterns on occasion.
Additionally, although each Doc Robot has two weaknesses, each attack can only do three points of damage (in a game where most main weaknesses do at least four). So not only are they harder to beat than they were in their original game, you also have to survive for longer.