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.
Alternative Character Interpretation: The ending's somber tone causes some to think that Mega Man is plagued with guilt over destroying the Robot Masters for the greater good. This interpretation was explored upon by The Megas in their Mega Man based rock opera.
The Wily Alien boss had the element of surprise, a gruesome appearance, and an awesome background to it's advantage. But it's just way too easy for a pivotal boss fight (and a much easier fight than the Wily Machine that precedes it). It has an insultingly simple attack pattern (fly in a figure-8 pattern and slowly shoot a weak, easily dodgeable pellet for each turn), and its only weakness is Bubble Lead (the weakest weapon in the entire game), which easily makes short work of it.
Wood Man has a fairly basic pattern even before you account for his having more weapon weaknesses than any other boss in the series.
Air Man can count if you have the Leaf Shield: wait for him to jump across to your side of the screen, then stand behind him and activate the Shield.
Complacent Gaming Syndrome: Most of the weapons are very good, and the game is generally considered to have one of the better weapon sets. Of course, none of that matters considering the Metal Blade is insanely broken. Many players prefer to go after Metal Man first because they want the Metal Blade.
Crowning Music of Awesome: Virtually ALL of the tracks, but especially Dr. Wily Stage 1 (a.k.a. Okkusenman). This game has more remixed music tracks than any other game in the franchise!
Demonic Spiders: The Sniper Joe mecha-walkers are giant monstrosities that replace the Giant Eyes from the first game. You're better off running into them to avoid fighting them — unless you have the Leaf Shield, which wipes out (just) the Walker in two hits.
Disappointing Last Level: After clearing the Wily Castle's exciting and challenging first few stages, the fourth stage is where things start to falter. You have to get through a puzzle stage outfitted with illusion floors and line-guided platforms; once you figure it all out, the stage becomes very tedious. To top it all off, you must fight the Boobeam Trap, which requires the Crash Bomber's entire weapon energy to defeat (a fact made worse as the only nearby enemies to item-farm from are Tellies and Sniper Armors). After that comes the series' very first Boss Rush teleport room in the next stage, which doesn't even have a segment giving you the chance to restock your weapon energy beforehand. You have to fight a battle of attrition with Dr. Wily once the Robot Masters are dealt with. Luckily, the last stage and its boss are far less brutal.
The Tellys. They're small tube-like bots that infinitely respawn. Avoiding them unless you need resources is the best solution.
Pipis. These robot birds drop eggs filled with about a dozen tiny birds which will Zerg Rush you. The ones in the ladder portion of Crash Man's level are especially annoying, because they're impossible to avoid without the Leaf Shield or Metal Blade.
When the game is paused, Mega Man's vertical speed is set to zero. Repeatedly pausing the game during a long jump will make Mega Man "glide" diagonally instead of falling parabolically, allowing for much longer jumps.
When pausing and unpausing, Mega Man will be in the "teleport" animation for a split second. During this time, Mega Man is invulnerable to all weapons. This glitch is the "Time Barrage" mentioned in the "I can't beat Air Man" song.
If the game is paused while Mega Man is equipped with a weapon that uses less than one bar of weapon energy per shot, unpausing the game will "reset" the bar he's currently on, thus giving potentially infinite weapon energy for those types. (In essence, this makes the Metal Blade even more of a Game Breaker.)
One peculiar glitch can be triggered during the Air Man boss battle: if you use Item 1 near the door inside Air Man's room, it takes you to a glitchy (but playable) combo of Air Man's stages sprites and the level layout of Skull Castle level 2, but you have to die in it to play the stage, as Air Man's preprogrammed air attacks won't subside without the stage resetting on your death. Unfortunately, it can't be beaten, because the stage boss doesn't show up at the end, forcing you to reset the game, and you can't play the stage without a Game Genie giving you item 1, which is needed to beat Wily Stage 2 and can only be gotten by beating Air Man (and beating him makes it impossible to access the glitch if you replay his stage again, because you automatically teleport out of the beated bosses room upon entry). See it in action here.
Getting enough objects on the screen animated at once could overwhelm the system's RAM, which could result in certain aspects of the game clock slowing down. In particular, a large number of enemies or a sufficiently large enemy (along with the flickering from Mega Man's Mercy Invincibility and a sufficient number of projectiles on screen) could trigger this. Clever use of the Quick Boomerang (easily the best for shooting many projectiles at once) could result in stretching said Mercy Invincibility much longer than it should ordinarily last. Due to differences in system architecture, this backfires in later rereleases.
It Was His Sled: No, Wily isn't actually an alien. The alien form in general counts, though: back when the game came out it was a huge surprise for obvious reasons, but now it's one of the most famous moments in the franchise's history.
Magnum Opus: For Keiji Inafune, to the Classic series and the franchise as a whole.
Polished Port: The Wily Wars re-release gave the game a 16-bit graphical upgrade, remixed music, and a save feature.
Scrappy Mechanic: The Bubble Lead counts due to how useless it is. Except for taking down the final boss, of course. Also: the disappearing blocks from Heat Man's stage.
Signature Scene: The opening is this for Mega Man 2, to the point where anything that pays homage to the 8-bit era has a high chance of beginning with an ascending shot of a building with the hero at the top. Even the promotional video for the Mighty No. 9 Kickstarter alludes to it.
The Boobeam Trap at the end of Wily Stage 4. Not only do you have to use Item-1 to reach the higher part of the chamber, but the boss can only be defeated by Crash Bombs, of which you only get so many. If you run out, you're fucked.
The only way to refill Crash Bomb energy if you run out is shooting hundreds of impossibly-placed Tellys and a bunch of Sniper Joes in narrow hallways in the hopes of getting the necessary energy capsules. You're pretty much better off killing yourself to restart the stage.
Quick Man's stage is notoriously irritating without the Time Stopper. There are two segments where you have to outrun a batch of instant kill lasers coming out of the wall, and you have very little room for error — especially with the second set. If you do manage to pass through the second set, you have a few respawning Sniper Joes in walkers waiting for you.
Heat Man's stage becomes this during the disappearing blocks segment (unless you happen to have Item 2 on hand). You need split second reflexes and knowledge of the exceedingly long block pattern, because one slip up will send you to your death. This segment makes the Ice Man and Guts Man stages from Mega Man 1 look easy.
Among the Wily Castle stages, stage 4 easily qualifies due to its tedious string of fall-through floors and line-guided platforms, constantly respawning enemies from all directions, and the Boobeam Trap at the end.