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.
Anticlimax Boss: One of the most recurring reviewer complaints. By the time the player has reached Capitol Prime, they've fought a towering mutant colossus, which has been clearly modified by Authority tech. For added difficulty, it is only vulnerable to the rocket launcher at certain times. And for the final battle... the player fights several waves of regular sized mutants, who have been clearly modified by Authority tech but easily dispatched by Sentries, Turrets, or the Infinity+1 Sword / Eleventh Hour Superpower that is the Authority Pulse Cannon.
Author's Saving Throw: The Scorchers DLC adds in features players wanted in the main game, primarily post-game free roaming.
The big heavily armored minigun guys that begin appearing about half way through the game. Rarely do they appear completely alone and may even show up in pairs alongside the normal enemies.
The Jackal clan sniper enemies. They shoot highly damaging rockets or fireballs at the player while their berserker buddies rush them with a barrage of melee attacks. On the higher difficulties these attacks can easily kill the player in just 2 hits by themselves!
The Authority mutants that (thankfully) only appear in the last level. They combine everything bad about a club mutant (see below) with decent armor and a powerful plasma cannon attack. Best hold down the trigger on that Authority Pulse Cannon if you hope to survive...
Fridge Logic: The Authority is desperately looking for Ark survivors and will go to any length to get it's hand on them, because Ark survivors contain the nanomachines that the Authority needs for various operations. Except it's later revealed that The Authority was started by a conspiracy of Ark survivors who rigged their Arks to reactivate sooner, allowing them to curb stomp any other survivor with their superior technology. This means that, logically, the Authority is supposed to have more than enough nanomachines already!
Somewhat following the last point: how is it that the Authority has so many advanced weapons and technology? They couldn't have built all of this in the years after their rise to power since the backstory reveals that the entire reason they rose in the first place was that they awoke sooner, presumably with loads of weapons and technology! How can this be true, if, as repeatedly mentioned on this page, Arks were not buried with weapons in them?
Definitely a case of All There in the Manual; the novel explains that Cross and his men rode out the apocalypse inside a "Super Ark" that was designed to house hundreds of high-ranking government members (Cross' people ambushed them and stole the Super Ark for their own use), and which presumably was better stocked with supplies.
Game Breaker: Once you get the schematics for the Advanced Wingsticks, you'll never shoot another bullet again. You don't even have to aim them. Just mash the button and three enemies at a time get instantly decapitated, and more often than not, you don't even lose the wingstick (that returns to your hand for another use). It doesn't help that all it takes to build them is three extremely common and cheap ingredients, and you can make fifteen with every such batch.
Goddamn Bats: The basic club mutants. They have low health, no ranged attacks, and no special powers, but are extremely fast, agile, and most often attack in large groups.
Paranoia Fuel: The game takes place after an asteroid hits the Earth — a very real asteroid, that might actually hit us. Thanks, id.
Of course the current probability of the asteroid hitting is currently 1 in 250,000, which are better odds than before when it was first discovered, and many believe that while it would bad if it hit it wouldn't cause any long-term global damage. Still, it is a bit scary to think about.
Scary part? In the backstory, while the odds of impact were rising higher and higher, the government was lying like a bastard 24/7, insisting that they were decreasing.
And even in a worst case scenario, it still wouldn't cause people to mutate, just starve to death mostly.
It turns out, however, that the asteroid isn't what caused the mutants. In an interesting deconstruction of the post-apocalyptic videogame genre, it is revealed late into the game that the mutants are failed experiments of the Authority's various attempts to create nanotech powered supersoldiers.
Sidetracked by the Gold Saucer: There are a wide variety of betting minigames and other distractions the player can engage in. Even worse, several achievements are tied to them and rely heavily on random chance to unlock. Hope you weren't doing anything important when you noticed the the new settlement you're visiting has a game you haven't tried yet...
That One Achievement: "JACKPOT!", one of the aformentioned luck-based achievements. It requires scoring four kills on your first roll at Tombstone, so start Save Scumming because the odds of getting four kills in one roll are 1 in 16.
The "Gotta Have Em' All" achivement is also a major pain to even attempt. To unlock it the player has to find every single trading card in the game all in one playthrough. These cards are almost always extremely well hidden in the enviroment or stashed off in a (possibly locked, hope you brought lots of lock grinders) supply room that the player is likely to miss. As frustrating as this would be on its own several cards become Lost Forever if not picked up during the one chance the player has to pass through the area. Needless to say, getting this achivement without a guide or walkthrough of some sort is borderline impossible.
Visual Effects of Awesome: The visual aesthetics and detail are impressive, and the game boasts some truly convincing mo-cap work.