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.
Gemini, from the first game, kills one of his allies for no reason when he could've easily helped her and defeated Mega Man. He also manipulates a boy with multiple personality disorder into helping him to blow up the entire planet and is revealed as the one who manipulated King Cepheus into destroying the AM Planet.
Mr. King is the leader of the organization, Dealer, and the Big Bad of the third game. Appearing to all the world as a benevolant millionaire who donates to chairty, in reality Mr. King is a Manipulative Bastard willing to use anyone for his own benefit. As the operator of Joker, all of Joker's crimes lead right back to King. In addition to forcing his own Wizard to self-destruct to defeat his enemies, King adopted orphans and forced them to undertake suicidal missions in order to further his own plans. In fact, it is said that Jack and Tia were the only orphans to survive these missions. He then proceeded to take control of Meteor G so he could take over the world by force, raining down deadly Noise upon those who would not subjugate themselves to him. However, after being betrayed by his subordinates, King who was supposedly destroyed, became an Energy Being and decided to wipe out the world using Meteor G because he figures that if he can't rule the world, he will destroy it.
Each rendition of the main theme, Shooting Star, is amazing. And then it goes vocal in the third.
Die for Our Ship: Many GeoxSonia fans despise Luna. In fanfics, she is usually bashed or treated like a spoiler brat. The fact that the anime turned her from a Tsundere to a Obsessed Fangirl with bits of Clingy Jealous Girl didn't help.
There's another case of this in the first game: it seems that Andromeda is a stupid name for a world-destroying war machine, until you realize that the FM-King's name, Cepheus, is also that of the mythological Andromeda's father, both of whom also are constellations in the sky to fit in with the theme.
The term "Brother" seems like a rather odd term to use to describe relationships with other people regardless of gender, but then you find out in the second game that Lan Hikari started the system, and he based it off his bond with Hub. You see, he notices that whenever he and Hub worked together, miracles could happen due to this "Link Power", and decided to try and connect the world through this. He succeeded, to say the least.
Also, 'brother' sounds like 'broader'. So 'brotherband' can be read as 'broader band', a pun on broadband.
Gemini Spark, Crown Thunder, and Hollow are all the most powerful fighters in their own class? Why? They're Elec-Type, which means that their powers are the closest to electromagnetism proper, where as all the other powers are modified into the elements.
Fridge Logic: Many moments from the first game become borderline retarded when you think about it. Wouldn't putting a car in the way of the truck have caused severe injuries? Was Sonia contractually obligated to give that concert, or not? (If she was, she could have been sued for damages. If not, she could have sued her manager. This may be a case of No Such Thing As Lawyers...) Why didn't the principal just make Mr. Shepar a Social Studies teacher? (Or barring that, that one teacher who teaches that nebulous class known as "Health", or even just Homeroom?)
They justify the bit about the car when Geo wonders if everyone's okay. Turns out they all got sucked into the computer system of the truck.
Also, the problem with Mr. Shepar's class (he does indeed teach homeroom - it's just all day with his one class) is that he's the one teacher at school who doesn't use the StudyWave as per the principal's desire; the principal gets fed up and blackmails him into needing to find a job to sustain himself and 7 kids.
Genius Bonus: Most players don't know what "Laplace" refers to, or even how to pronounce it.
The villain of the second game and her Dragon both draw from the mythology of the Tanabata festival. Their english names draw from the stars featured in the myth.
Ho Yay: Oh lord, the Gemini Spark chapter of Star Force, between Pat and Geo. The first part of which is more or less Pat and Geo going on a date together and then Geo shyly and awkwardly asking Pat if he wanted to be "Brothers" afterwards.
Geo was extremely depressed over Ace's death.
Geo and Jack in 3. More a case of Foe Yay, it starts off with Geo trying to befriend Jack. Then Jack seems to start finally warming up to Geo after they hang out in swimsuits at the beach. Then after The Reveal, Jack spends the rest of the game obsessed with trying to kill Geo (not defeat, kill), only to fail utterly to stop Geo from ruining all his evil plans at the last moment... then within a few minutes, gives into Geo's will, leaves with his sister back to earth, and eventually works to save Geo's life after he's left out in space. And according to the credits images, does become at least friends with Geo.
In the anime, for Gemini, it's either when he just starts killing the FM-ians, just when he kills Wolf, or when he kills his other half.
Scrappy Mechanic: The SF1 games had levels that fell into the same rut that many other Nintendo DS games fell into early on, with level puzzles relying largely on Touch Screen gimmicks rather than button pressing. The SF2 games did away with this at first except for the The Final Dungeon. Remember those sections where you get chased by Murian guards? If you touched them, you will initiate a minigame where you need to draw lines on the guard with the laggy touchscreen function. In less than 5 seconds. Otherwise a fight ensues. They are rather tough with a lot of hitpoints. Oh, did I mention to get to the Final Boss you need to sneak through those guards? If you lose the Le Mu fight, you have to cross the dreaded section all over again! Now they wonder why the fans are peeved...
Ship-to-Ship Combat: Between Geo/Luna and Geo/Sonia shippers, sometimes elevating to idiotic heights.
That One Boss: A few opponents have the chance to become this during the games, though like the Battle Network games most of them are either fairly easy or are souped up bonus bosses. Star Force 2 has a combination of Goddamned Boss and Bonus Boss that takes the cake though for possibly the entire series. After completing all of the bonus content, facing the final boss again results in a mandatory souped-up encounter. Winning that, unlike every other Battle Network and Star Force game, results in Solo deciding that he wants to have a real final battle with Geo, instead of just leaving for when Geo's ready. Cue the battle with Rogue SX, who is so stupidly fast and powerful chances are the battle will last only a few seconds before you're just dead—if you can even survive a combo from him. Your only chance against him is either being really good with countering him(Mad Vulcan three works particularly well), stun lock, or cheating. What makes this battle even more rageworthy is that if you screw it up, you have to go back, beat the souped-up final boss again, and watch the unskippable credits, to fight it again.
Zack, thanks to the events of the start of the first game. He still suffers from it, but people have started to like him for his roles in the later games.
In the western fandom, Luna garners a large hatedom, largely due to being the unpopular choice for the series' Ship-to-Ship Combat (see Die For O Ur Ship) and the tendency of those with Shipping Goggles to oversimplify/downplay or misconstrue her Character Development. The rest of her haters are simply sick of the Tsundere archetype. This is averted in Japan, where she has as much popularity, if not more, than Sonia.
They Changed It, Now It Sucks: Well, it is Mega Man. One of the main issues the fandom had with the new series was the new battle system, which stripped out much of the logistic and strategic complexity of Battle Network in favor of gameplay that heavily relied on timing and reflexes. Its detractors refer to the new battle system as a watered-down imitation, while its fans have actually compared it to the reflex-based gameplay of the main series' timeline.
Fans weren't in particular sure whether they preferred old Mega with War Rock's head for a blaster or new Mega with a much more streamlined variant.
Combined with It's the Same, so It Sucks, the entirety of SF2 is this. The gameplay is too similar to SF1 while straying too far from the core plot (no concern of space at all contrast to the first and third games) makes SF2 the textbook definition of failure among the fans.
Viewer Gender Confusion: Pat (as in Patrick, not Patricia) is dressed in purple spandex, and wears a purple headband with long hair. His androgynous name was probably an intentional carryover from the Japanese version, where he was named Tsukasa, a common Japanese name for both genders. To further the point, the name Tsukasa is usually written in hiragana if it belongs to a girl, and kanji if it belongs to a boy. But Tsukasa Futaba Takes a Third Option and writes his name in katakana. In fact, there's fanart featuring him as a girl that was produced before the first game came out.