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 is 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 The Fist of Mars in motion.
Ned Noachim holds a vicious prejudice towards Martians and is introduced attacking a hospital to steal medicine and have his way with the nurses. He is implied to blow up the hospital to frame the Born In Space (BIS) group and later kidnaps three orphans from Pandora Frettum and places them into unmanned LEV suits set to explode when destroyed in order to sully BIS's name. Noachim forces his own soldiers to explode rather than surrender.
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.
Just Here for the MGS2 Demo: Most likely Metal Gear Solid fans were likely thinking "Hey, the $50 MGS2 demo came out!... What? There's a game about Humongous Mechas included with it? That's pretty cool, I guess... I'll try it out after I beat this demo twenty times."
Most people also buy the HD Collection just for The 2nd Runner alone. The PlayStation Store also carries the HD Edition of each game individually, so it's no surprise which game will sell more than the other.
Moral Event Horizon: Baan removing a little girl's oxygen mask and shooting into a crowd to get information.
Viola shooting Celvice in the first game. Fortunately, Celvice lives but that was one heck of a Kick the Dog moment.
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: The HD Collection suffered from technical and frame-rate issues on both the PlayStation 3 and Xbox 360, but the former's version of The 2nd Runner was hit the hardest. The PlayStation 3 version suffered from frame-rate stability issues running at most 30-40 FPS (if not less) whereas the Xbox 360 version ran at 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 Konami's 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. Unfortunately, Xbox 360 owners won't be getting the patch.
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 was 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.
Sequel Displacement: When it comes to the Zone of the Enders games, The 2nd Runner is almost always the one that comes to mind. The sequel was praised for fleshing out the potential of the first game had and making it much more action-oriented, while the first game is considered average at best and its main selling point to Metal Gear Solid fans was the demo for its sequel.
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 sub-weapons work on him. Its zig-zagging homing lasers are a bitch to dodge moving around all sorts of directions and the damage is punishing if you get caught into a barrage of them. As Aumaan Anubis, its Burst Shot homing capabilities are even persistent, so simply trying to dodge isn't going to cut it unless you shoot it. Worst sill is Aumaan Anubis' ability to recover energy while protecting itself in an impenetrable shield if you don't shoot down the Aumaan panels.
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.
That One Side Quest: The S.O.S. missions of the first game. Basically you have to clear out the enemies taking over a particular area while avoiding collateral damage. Sounds easy at first until you find out that giant mechs aren't good at preventing the latter. Often you're liable for something to go wrong and you'll be penalised for it, be it one misfired attack or enemies attacking a certain section of the area that you couldn't get to in time. Skipping the missions outright doesn't help if you're trying to get the good ending as civilians and buildings will be wasted over time if left unnoticed.
They Just Didn't Care: Konami hiring High Voltage Software, a company known for making terrible games, to handle the HD ports of the PlayStation 2 originals shows they didn't try to make a proper port on two powerful consoles. If you're Xbox 360 owner, Konami won't be releasing the 2.0 patch for you.
Wangst: Leo in the first game goes on and on about not wanting to kill, even late in the game. What makes this especially egregious is that most of the opponents he fights are unmanned units.
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.