Bag of Spilling: Mega Man lost the ability to swim from Mega Man 8. A few items from the eighth game, too, have been removed in this journey that were there.
Bait-and-Switch Boss: King Stage 1's boss, Atetemino Proto, a bagworm robot. At first, there is annoying, trolling chimp named Monking A that deceptively looks like the boss, but shooting it only causes Monking A to temporarily be eliminated, then respawn. standing on a platform attached to a pulley system weights it down and dredges up Atetemino Proto from under the lava so you can open fire on its head.
Many of the data CDs have rather nonsensical translations. For example, Pharaoh Man's Bad Point is translated as "Too nice to women" when it was originally "Weak to Beautiful Women", while Dr. Light's Bad Point is (rather infamously) a simple, contextless "Douchie" (which was supposed to be "naive").
Also from the same port is the instruction manual. Auto is referred to by his Japanese name, Lightot, and "Wily" is misspelled "Wiley" as in the third game.
The intro stage is one big Continuity Cavalcade of previous games in the series. There's a fire portion reminiscent of Fire Man's stage from 1, hallways filled with drilling Moles like in Metal Man's stage from Mega Man 2, a rainy segment similar to Toad Man's in Mega Man 4, a ship with rising and falling water from Blizzard Man's stage in Mega Man 6, and finally at the end you fight a toned-down version of the Green Devil from 8.
The last level has a Boss Rush as usual, but the bosses are fought sequentially with platforming sections in-between - just like the first game.
Chest Monster: There are chests throughout the game that contain power-ups or CDs, but some will come to life when shot and are very aggressive.
Combining Mecha: The three minibosses of King 2, Ground Tank, Air Tank, and King, combine to form the boss of the level.
Astro Man and Tengu Man are bosses from Mega Man 8, although their attacks and patterns (and weapons) changed.
King uses the Gemini Laser from Mega Man 3 during the fight with him. Luckily, it doesn't hit as hard.
Damn You, Muscle Memory: Just like in Mega Man X, Bass can dash by pressing the dedicated dash button, or by double tapping forward. The Game Boy Advance port doesn't have a button, so you must double tap. That split second will result in countless mistakes and deaths. Thankfully, Capcom would later remap the dash to Down + Jump in Mega Man 10, the same command for Mega Man and Proto Man's sliding.
Demoted to Extra: So where was Proto Man in all of this? He was fighting King at the robot museum where he got chopped in half. He got repaired just in time to exhaust himself by destroying King's shield and then snuck into Dr. Wily's lab to destroy all the data he had on King. But he's not playable. This did end up resulting in at least a couple of rumors that made the rounds claiming that Proto Man could be unlocked as a playable character.
Denial of Diagonal Attack: Mega Man still has this problem. Bass doesn't. The Magic Card can be fired upward and the Ice Wall slides along the ground, though. The Wave Burner covers the floor and can destroy some otherwise invincible ground enemies.
Divergent Character Evolution: In Bass' previous appearances (as well as his playable stint in The Power Battle and The Power Fighters), the Bass Buster functioned identically to the Mega Buster. To differentiate Bass from Mega Man (and make things fair considering his vastly superior mobility), his Buster was drastically altered, which stuck for Rockman & Forte: Challenger from the Future and Mega Man 10.
Hijacked by Ganon: King eventually realizes his master and creator, Dr. Wily, lied to him about the nature of humanity. At this point the good doctor shows up, ups King's brainwashing levels, and retreats to his fortress.
Hopeless Boss Fight: King's Tower Shield is indestructible. The first phase of the fight involves waiting him out and dodging his attacks. Finally, Proto Man shows up and destroys the shield to give you a fighting chance.
The boss of the first fortress stage. You must balance yourself on a pulley with the boss above an acid pit. Once your side is low enough, the boss will emerge and you can attack it. When you kill the boss, the platform you are on will sink instantly, and if you don't jump to safety then you will burn in the pit as the boss dies. Strange because during the fight itself you will take damage instead.
Bass: So, you intended to use King to take care of me, did you? You dirty son of a bitch!
Pyro Maniac: Burner Man, if his concept art◊ is any indication. You also fight him in a forest. Apparently King tricked him into believing that he must burn a forest daily or a bomb inside him will explode.
Right Makes Might: Proto Man gives Bass a lecture during his ending that is pretty much this. He says that Mega Man will always be the better fighter because he fights for a just cause, while Bass only fights to satisfy his ego.
Schrödinger's Player Character: No matter which character you play as, you must defeat all the Robot Masters and raid King's Castle. The other one never shows up.
Road Cone: Mega Man 9 implies that the canon path was Mega Man's. Bass's ending seems to have happened though.
Sequel Difficulty Spike: Megaman 8 had checkpoints, simple boss fights, loads of extra lives, and had no penalty when you get a game over. It was the easiest game in the franchise. And then came this game.
This Is a Drill: Ground Man uses the Spread Drill, which can bisect twice to cover a lot of room. He will also drill into the ceiling, dig above you, and then drop a MASSIVE drill from above on you. He can even transform into a Drill Tank.
Underground Monkey: infamously, the Wily Machine and Capsule here are basically the same ones from 8, with a few aesthetic changes and new attacks.
Warmup Boss: And it's the Green Devil, of all things. Thankfully, he doesn't split up this time round, and just stands there during the whole battle.
Woobie, Destroyer of Worlds: Dynamo Man's resentment of humanity and primary motive for aiding King's army is that his unstable electromagnetic force field (courtesy of King tampering with him) makes it lethal for anyone to get close to him. As a result, the robot whose former job was giving tours of a power plant to schoolchildren is forced to live in solitude.
Xanatos Gambit: Dr. Wily had his bases covered. Either Mega Man would perish or King would destroy Bass and grow stronger. Or Bass would destroy King and grow stronger. Or Wily would collect all of the robot data King collected and start working on a King Mk II. Bass's ending shows Proto Man ruined the last outcome.