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.
Hiai Naru Tougi from Idolo/Dolores, i is intense beyond all rational thought.
Best Boss Ever: Despite being a fairly easy (or downright hard in the Special Edition) boss, the battle against with Leo and his Vic Viper in The 2nd Runner surely counts as one, especially if you're a long-time fan of Gradius. The boss music, the attack patterns, everything about this boss battle is one big Shout-Out to Gradius.
Nohman Ridley, the leader of the extremist Martian faction called BAHRAM. He causes countless destruction in the name of freeing Mars and has no qualm about sending his minions to death in order to achieve his goals. Then, it is later revealed that not only does Nohman not care about Mars' independence at all but also wants to wipe out the entire solar system with the Aumaan. Even if one takes madness induced by the Metatron into account, it's clear that Ridley is a power-hungry madman who will stop at nothing to achieve his ambition, as shown when he sent Dingo and his teammates on a suicide mission just so he can eliminate competition for the leadership in BAHRAM. This particular incident happened before Anubis and Jehuty were made.
On the Earth's side, we have Zephyr, the Mad Scientist. Willing to do anything to gain recognition for his research on Metatron, he uses children in lethal experiments to develop the mindflow system, which subdues the will of a pilot to enhance the performance of orbital frame. This system works better with children, making them ideal for soldiers. Only two of the children, Pharsti and Vale, he used for his experiment manage to survive and run away, setting the plot of Fist of Mars in motion.
Ned Noachim meanwhile is a Complete Monster on a more personal scale. This guy takes sheer pleasure in depriving a hospital of life-saving medicine, watching a city burn, and holding three orphans and an orphanage hostage with explosives, among other horrific things.
Hilarious in Hindsight: At one point during Dingo's exchange with Leo in The 2nd Runner, Dingo joked about selling Jehuty "at a high price". Take a wild guess which game made that line infamously funny.
Also Bolozof and Cage have a little of this a third of the way into The Fist of Mars. Mostly from Bolozof, though.
It's Short, so It Sucks : You can beat the first game in as little as three hours if you know exactly what you're doing and where to go, thanks to most of the game being padded with backtracking and fetch-quests.
The 2nd Runner's English localization also has its moments, from Ken's battle cry to Dingo yelling "You devil!" to Nohman, due to shoddy translation effort (which is a stark contrast to the localization of The Fist of Mars).
Needs More Love: Dolores, i. It borders on "Like It or Hate It" with some areas of the fandom since the titular mech is pink and the show itself not being like other mecha anime series (such as Gundam), yet that's what makes the series stand out (not the whole "Dolores being pink" part). Unlike most typical mecha series centering around an adolescence with the coming of age story of its time, here we have a middle-aged space trucker and veteran soldier trying to reunite his family and reconcile with his estranged children, and he's willing to go through hell and back to do it.
Play the Game, Skip the Story: The first game seemed to be along the lines of an emotional tale of war and the value of life, but due to the mediocre voice-overs and shoddy script translation, most people outside Japan skip the story of the first Zone of the Enders altogether.
Porting Disaster: Shockingly, the PlayStation 3 version of The 2nd Runner in the HD Collection suffers from frame-rate stability issues, running around 30-40 FPS whereas the Xbox 360 version can run at most 50-55 FPS until the action really intensifies; the frame-rate on the PlayStation 2 originals still runs better than both versions of the HD Collection, going against their original promise of presenting the games in full 60 FPS. The PlayStation 3 version is still playable, but it could a nuisance to players at any moment where the game bogs down when a relative 40-60 FPS is a must.
Kojima Production has stated in a recent podcast that they are working a patch for PlayStation 3 version of the HD Collection to address these problems. Unfortunately, thanks to the damage done by High-Voltage Studios, they have to re-work the games from scratch to fix them, thus putting production the series' third entry on hold for a while; no word on planning to fix the Xbox 360 yet either.
Anubis and Aumaan Anubis in the final areas of The 2nd Runner. You only have Zero Shift available, all other sub-weapons had been destroyed by Aumaan, including Vector Cannon which could bust through the boss' shield with ease.
That One Level: Any time there are friendlies, but especially the massive battlefield clash in The 2nd Runner. Not only are Jehuty's controls not made for avoiding collateral damage, ADA isn't too picky on what she locks onto. This creates one of the few cases where things would be substantially easier if they'd just let you fight an army at once on your own. Also, to get an S rank, you must beat it without anyone dying.
The Homing Missiles might help, but can be taxing your sub-energy... unless you're NakedJehuty.
The Scrappy: Despite going through post traumatic disorder, Leo became the gaming equivalent of Shinji Ikari due to how he is against fighting and his multiple arguments with Elena and company. The English voice acting did not help at all.
However, he is Rescued from the Scrappy Heap in The 2nd Runner where he is not only hotheaded, determined to save ADA, a skilled pilot regardless of piloting a weaker Frame, an important supporting character but also has one more passable English voice. In Japanese, he is voiced by Kenichi Suzumura.
What an Idiot: Dingo, if you want stop Nohman from killing your old man, yelling "Stop!" while reading the super-fast Jehuty is really stu... oh wait a sec, he really stopped... you two really are an idiots.