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.
Breather Boss: Toad Man, since he can be looped into an infinite where he does nothing but jump. Pharaoh Man too if you use his weakness (he becomes a sitting duck), and Bright Man if you know how to stop him from using Flash Stopper.
Fanon Discontinuity: Some hardcore fans like to consider Mega Man 3 the true final game of the Mega Man Classic timeline, preferring to assume Dr. Wily died at the end of 3 and ignoring everything from 4 onwards. (some less hardcore fans like to consider the same of Mega Man 6, and ignore everything from Mega Man 7 onwards)
Fridge Logic: Why is Pharaoh Man weak agains bright lights when he's using a fire based weapon that also emits a bright light?
Fridge Brilliance: Flash Stopper is a time based weapon. Pharoah Man is essentially a mummy, whose bodies degrade over time.
Bright Man may just be able to flash a light so bright, it overloads the optics for a while. Fire doesn't necessarily mean bright.
That One Boss: Pharoah Man if you don't have his weakness (you do and he's a pushover), as he's really fast and hits hard.
Also Bright Man, who can stun and then jump on you for massive crash damage. Unless you know he only uses Flash Stopper at specific HP intervals, then you can shoot him with one uncharged shot and take him down with nothing but charged shots or Rain Flush in relative safety.
Then there's Ring Man, who can cause huge crash damage and counterattack if you shoot him on the ground.
The Wily Machine, if you don't know that you can detonate the Drill Bomb in mid-flight. This can lead to having to resort to Outside The Box Tactics such as trying wire, Rush Jet, or Rush Coil in an attempt to hit that just-out-of-reach weak spot.
That One Level: The end of Bright Man's stage is very difficult and frustrating. You have to jump on moving platforms while dodging the projectiles of the Lightbulb bots. Oh, and don't shoot said bots, as they will black out the screen.