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.
Goddamned Bats: The toy soldiers can latch on to you, immobilize you, and steal bolts.
Good Bad Bugs: Speed Runners have found out that you can double jump with the Lightning Bolt. You can also wall zip by jumping during the lightning bolt into a wall, as the wall will try to eject you. Great for Mega Man.
Porting Disaster: While the Game Boy Advance port isn't bad overall, Bass' dash move does not have a set button on it, unlike the Super NES original. This leads to the dash taking slightly longer to execute and more slip-ups.
The music isn't quite as good thanks to the GBA's sound chip being inferior to the SNES' chip.
That One Boss: Burnerman. He has a charging attack that's tough to dodge and deals a ton of damage, his Wave Burner can block your shots and pin you in a spike-filled corner, and he sets beartraps that grab and hold you, leaving you wide open to attack. Also, there's the issue with his weakness; while most bosses in the series will let you get away with just spamming their weakness until they're dead, Burnerman will not. Fighting him with the Ice Wall turns him into a bit of a Puzzle Boss that requires you to push the wall into him, forcing him into the spikes on either end of the room, a task that's easier said than done.
The other major candidate is Dynamo Man. Unlike Burner Man he is very vulnerable during most of the fight. The problem is he spends most of the fight in Beam Spam mode. He also forces you into a Sadistic Choice of forcing him to fire hard-to-dodge projectiles, or guessing where his Lightning Bolt will strike with no warning (there is a pattern to his Lightning Bolt, but it's incredibly hard to pick up on, requires split-second precision, and you can mess it up by walking just a few pixels too far). Finally, he will jump into a recharging station partway through the fight and will completely heal himself if you don't destroy it quickly. The Copy Vision will trick most of his attacks and let you focus on dodging the rest, though.
Magic Man loves counter attacks, and all of his attacks require a different response. The Tengu Blade must be properly timed so you hit him and not his projectiles. Sliding through him with the blade deals extra damage (and he drops his cards!) but you have to start it RIGHT in front of him or you'll take Collision Damage.
There's also the King Jet. You have to fight it on an Auto-Scrolling Level, having to constantly jump from one small platfrom to the next. The Jet itself does everything in its power to make you fall, including sending out flashbangs, a Rocket Punch that destroys any platfrom it collides with (often the one you just started to jump to...), and finally the above-mentioned Wave Motion Gun, which can at least be countered by destroying its power crystal before it finishes charging. The Jet has no apparent weakness, and no lifebar so you can't even tell if you're doing much damage or not. At least the game was kind enough to make an infintely-spawning 1-Up appear shortly beforehand so you can retry the battle as many times as your sanity allows.
To make matters worse, the boss is even harder when you're Bass. The flying platforms are spread further apart, forcing you to double jump the whole time.
That One Level: The second level of King's fortress could have been broken up into three levels easily. In fact each section ends with a boss: King Tank, King Jet and King himself. The King fight is also three phases long, just to add to your misery.
The third and final fortress level isn't much better. This stage includes the inevitable Boss Rush, but rather than fight the robot masters in a teleporter room as usual, it goes back to the Mega Man 1 method of fighting each robot master one at a time throughout a Marathon Level which is particularly brutal for Mega Man due to some of the platforming segments (Bass can use Treble Boost to fly over most of it). Finally, there's the two-part final boss fight with Dr. Wily at the end, and by then you're likely hurting for health, energy, and possibly lives, due to few refill opportunities being made available throughout the stage.