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.
It probably didn't help that those two either didn't make it outside of Japan or if they did, weren't around for long. The novel was actually not published in English until 2007, and it's rather rare in a lot of North America.
The awesome final boss theme, "U.B.", and also "Escape from U.B.", a creepy song which really provides extra tension during the final escape sequence.
Game Breaker: The Super Toolkit available in New Game+ (aka "EX Mode"), although the upgrades are still limited by the attribute "donor" items and the upgrade capacity of the target. And whether you collected all of the Rare Trading Cards for it; miss a few and you'll be awarded a lesser version that destroys donor items.
You play your cards right, you can put together a pretty cheesed up weapon on your first playthrough. How about a handgun that fires two salvos of flaming shotgun rounds? Yes please!
In an LP, the player managed to put together a gun that fired grenades full of acid and liquid nitrogen in shotgun spray.
Upgrading a gun's ammo capacity and range to high enough levels can let you attack monsters from any spot on the battlefield (unless they fly/dig off screen) and never having to reload.
Adding the shotgun effect to regular rifles or handguns makes the things effectively fire flechettes for full effect in a cone, neatly breaking the rate of fire problem noted in Awesome but Impractical.
Guns that have the "Enter 2 (or 3) Commands" effect can offset the rate of fire problem described above, allowing you to shoot multiple times but have the attack power be based on a single bullet per shot instead.
Even moreso, you can and do use a Power as a command, meaning that that mod can have you fire off multiple powers, possibly mixed with gunfire.
Powering up your armor enough can let you be completely immune to damage from almost every enemy attack and you will need it when tackling the higher levels of the Chrysler Building.
You can also modify your armor to make you immune to every single status ailment in the entire game, with the exception of Defense Down.
The Woobie: From what we learn of her, Melissa Pierce. She was an Ill Girl since her youth and all the way up to adulthood was hooked up on medication. Despite that, she struggled to become an opera singer and had to share her part with someone else. And then on her opening night, she was taken over by Eve thanks to a kidney transplant supplied by Maya back in her youth as well as further medication by Klamp that would make her body even more susceptible to Mitochondria Possession.
Unwinnable by Insanity: After defeating the Ultimate Being, it starts to chase after you and gradually picks up speed. When you reach the boiler room, Aya notes that she should overload it so that the ship explodes and kills the creature. However, you can actually skip the self destruct sequence and keep going. If you choose not to blow up the ship, the creature will move so fast that it will catch up and kill you instantly no matter what you do. Only by rigging the ship to explode will the creature move at a pace that keeps you on your toes yet still give you a chance to escape.