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.
Funny Moments: In Slash Beast's stage, the first repliforce mook that destroys the train connectors also falls into the pit he created.
Game Breaker: The Force Armor in general, but especially the head component, which gives you unlimited ammo for your weapons. Charged attacks still drain your energy, but the charged attacks are generally considered to be overkill anyway, and the ability to spam the normal versions of the attacks with impunity is far more practical.
Colonel's Sword Beam flurry has an odd blind spot: right in front of him. Apparently you can stand right in front of him and not get hit.
Zero's Slash Dash Cancel started here. You can Lag Cancel the first slash, and cancel the sword cancel with a dash. You can then cancel the dash with a slash. With proper timing, Zero won't move from his spot and will just Blade Spam. Bosses don't trigger Mercy Invincibility until Zero completes his combo, so Zero can shred most bosses in about 4 seconds. The only exceptions are airborne bosses or Zero getting hit. Mega Man X6 forced lag after enough cancels to try to fix it but it's still effective in X4, X5 and X6.
Growing the Beard: It was with this game where the X series' stories got more complex, the levels got bigger and more elaborate, and Zero's sword-based playstyle was introduced.
Magnificent Bastard: Sigma with his trick manipulating the Repliforce, which he pulled off without the Maverick Hunters having any idea he was involved. The plan to hijack Repliforce's Kill Sat nearly works in spite of X and Zero's involvement only being thwarted by a last minute Heroic Sacrifice by General.
Magnum Opus: Competes with X1 for being the best in the X series.
Marathon Boss: Sigma has three phases in this game. The first one can be resolved quickly when you use fire attacks. The second one relies on manipulating his scythe so he goes for an easier to avoid attack. The final form has three forms he randomly switches between: A gun form that takes its sweet time lining up shots, and a garbage form that sucks in debris from random angles and blows you towards Spikes of Doom. There is also another form consisting of Fire, Ice, Lightning heads that Beam Spam and cannot be permanently destroyed. With only two energy tanks it's clear Sigma's strategy is to just stall for time and hide his weakpoints for as long as possible. Makes sense, since he's activating Final Weapon.
Strangled by the Red String: Zero and Iris together don't have much screentime to suggest that they're attracted to each other, at least not until the latter's death. Xtreme 2, which is a prequel in which Iris appears, doesn't give much hints either.
Surprisingly Improved Sequel: Though fandom is divided as to whether this game is better than X1, nearly everyone will admit that it's a major step-up in quality over X2 and X3.
Magma Dragon comes to mind first. You can bring a Ride Armor to the fight with him is probably lampshades how tough he is. His fireballs are surprising fast for Zero to avoid, and his jump kick and Breath Weapon ensure X needs to stay relatively close to react properly. His Desperation Attack is a Meteor Swarm that is very hard to react to while he's shooting more fire everywhere. Zero never gets his weakness (Storm Owl's projectile parry technique does NOTHING to this boss) so it's a straight up brawl. Your first time through will likely hit a roadblock during the Boss Rush, because you don't get a Ride Armor there.
Fight Storm Owl without Aiming Laser. He has a surprising number of attacks that come in from different angles and it's easy to get trapped. He flies around the arena and quickly leaves or raises a barrier when hit, so he isn't vulnerable most of the time. It's even worse with Zero, who has to get close without getting hit himself. Zero's Rakuhouha deals extra damage and stuns Storm Owl immediately, but the ammo is so limited it's best used as a panic button to avoid traps, rather than actually deal damage.
When the Sky Lagoon crashes into the Earth, Colonel could have went along with the investigation and clarified that the crash wasn't their doing, or if he felt that any investigation would be unfairly biased, clearly state this. But he says that warriors don't disarm and leads to his entire army being branded as Mavericks.
Sigma seems to be the only smart person in this plot, as he played everyone into the Honor Before Reason trap and only lost because X and Zero could beat him in a fight and General was functional enough to perform a Heroic Sacrifice.