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.
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 for 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.
Polished Port: PlayStation 3 version of The 2nd Runner after the Hexa Drive patch. The 2nd Runner now runs at the intended 1080p quality with smoother frame-rate oppose to being up-scaled at 720p with frame-rate issues (see below). Xbox 360 owners are unfortunately left out.
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 (if not less) 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 problems in the PlayStation 3 version of the The 2nd Runner was finally addressed in July 2013 with Hexa Drive's 2.0 patch; the downloadable version of The 2nd Runner and the Japanese PlayStation the Best edition copies of Zone of the Enders HD Collection will have the update ready from the get-go. Doesn't seem like they care to fix the Xbox 360 version, though...
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 hot-headed, but is determined to save ADA, and 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.
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. In the time trial mode, none of the subweapons work on him.
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, and 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.
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.