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.
The game's lack of a manual save feature. The developer was unable to implement one due to budget restraints. Nonetheless, some fans are insisting that this ruins the game, while others are willing to put up with checkpoint saving. This was fixed with the release of the Dragonfall DLC.
Some like that the $20 price includes a level editor that allows the community to create an endless amount of content for their characters. Others are crying out that the developers are letting the community finish the game for them.
Complete Monster: Dr. Holmes a.k.a the Emerald City Ripper. He took over the mental hospital and used its patients for organ trading and grisly Body Horror experiments, which included making designer sex slaves out of them by constructing a body out of various parts, sticking a head with the desired face on it and overriding the brain with chips.
It should be noted that this is relatively tame by Shadowrun standards and could in fact be considered business as usual for many doctors. It also should be pointed out that he is only the first villain you end up putting in the ground. Yes, the Universal Brotherhood is that bad.
One mission in Dragonfall has taser-wielding junkies, which do up to 3 AP damage. This stuns any character they manage to hit, and a junkie can keep that character locked down indefinitely. This wouldn't be so bad normally, but you're in the middle of a Hold the Line mission being flanked from two sides while defending a fragile target from drones that hit twice in a round and trying to keep the junkies from hacking the two consoles which are making the mission bar progress. Seriously, kill these guys on sight.
Any monster with a DoT effect like acid or poison is automatically twice as annoying as enemies who don't have it. This is because magic or end-of-round healing is based on the last hit taken, and DoT effects usually do a fair amount of initial damage followed by paltry DoT damage that prevents you from restoring the big loss without wasting a medkit. It certainly doesn't help that magical creatures with this effect are usually harder to kill than humanoid enemies, and are blessed with better aim.
Disappointing Last Level: The final mission of Dead Man's Switch is a grindy trip through an underground maze filled with Demonic Spiders and very little plot or character development. The final mission of Dragonfall is a lesser offender by having more plot development and less annoying foes, but it's still debatable if the undergound maze section was really necessary (at least you can traverse it quickly when you know what to do) and opinions on the final boss (specifically his game mechanics) are split.
Most moves that manipulate AP effectively give you extra turns. The wall conjurations of the shaman are also very useful, since they can pin down an enemy as you surround them, lock down a hallway or even be used as cover. The AI also likes to cross them, which is also a winning situation for you, especially with the walls that substract AP.
Auto Reload is a pistol skill that can be unlocked as early as the 4th level in the Karma system. It removes the AP cost for reloading. With this skill, you can keep firing your pistol for as long as you have AP, which is really gamebreaking when you take into account the fact that several weapons and high AP skills use your ammo capacity as a check against you abusing them. This makes revolvers very useful as it averts their short clip capacity handicap and effectively turns your character into The Gunslinger. Once you have maxed out your pistol skill, you effectively have a high chance of scoring critical hits on your enemy while never having to reload. This is balanced by the fact that pistols are the only gun category with the ability and are on the low end of the damage scale.
Physical Adepts went from being largely thought of as underpowered when Dead Man's Switch was released to perfectly serviceable in Dragonfall to easy capable of breaking the game in Dragonfall: Director's Cut. Partially thanks to the bioware available from Doctor Ezkibel's new sidequest, it's relatively easy to fashion a build that gimps the tougher encounters in the game with a player-character that has a high chance to dodge, a high ability to withstand hits that aren't dodged, and high damage output.
Good Bad Bugs: From the Dragonfall campaign. For whatever reason, Audran is sometimes incapable of opening dialogue with the player during his initial appearance; If this happens, he remains a "neutral" character for the rest of the battle, and follows the player around without attacking them.
Iron Woobie: Glory. She's a nearly soulless husk due to the bulky, outdated, Essence-costly bioware mods she's been modified with. She had to do this in order to escape from the influence of the Adversary. And that's just one part of her Dark and Troubled Past.
Audran crosses this when he launches an attack on the Kreuzbasar, killing dozens if not hundreds of people who had absolutely no idea that his organization even existed, including Goldshmidt and Kami. And especially when he personally murders Paul Amsel.
The Director's Cut edition of Dragonfall includes an extra mission that serves as this for Luca Duerr. It starts off with him just sending you in to set up surveillance on a supposed enemy of the Flux State. Turns out what he actually had you do was plant a bomb to blow up the building and kill everyone inside it. On top of this, he engineered things to go wrong at every opportunity, just to see how the Player Character would adapt, made the whole thing a Batman Gambit to kill two of the people he hired for the mission, and even tricked a normal working class dwarven woman into being an accomplice of terrorism purely For the Evulz.
Paranoia Fuel: One mission has you storming a corporate building to stop some immoral blood magic research. It is possible for you to steal the research data and sell it for cash. The research in question? A magic that will allow the user to kill a person, no matter where he or she is, so long as the user has access to a blood relative...good luck sleeping if you let that knowledge get out there.
APEX. She can find you anywhere on the net and fry your brain so fast that you can't even jack out. If you don't kill her, you're forever at her mercy, because betraying her ensures that you and anyone you know can never go near the Matrix again.
As of the Director's Cut of Dragonfall, the Black Lodge. An Ancient Conspiracy that wants to take over the world. And according to Dietrich, if you take their money, they as good as own you. And they warn you that while they don't mind you passing up on one or two of their optional objectives, their patience has their limits. As if you didn't have enough enemies in Dragonfall.
Harrow's camp. It seems like such a nice place. Because there's a corrupted spirit whispering in the back of your mind to make you more obedient. Enough to make you a sex slave or partake in a human sacrifice.
Scrappy Level: The "underground maze" section of the final level in Dragonfall. Filled with Demonic Spiders, dark, labyrinthian and difficult to navigate, with many areas serving no apparent purpose but to mislead you, and most importantly, breaking climactic tension by coming right in-between the Big Bad's Motive Rant/reveal of the Evil Plan and the Final Boss.
Scrappy Mechanic: Decking is the least popular aspect of the game. The combat system in the Matrix is similar to that in meat space, but it's much more simplistic. You'll usually only jack in one person at a time, there aren't many tactics to utilize, level layouts are pretty basic, and just about every enemy can be killed with a few normal attacks. It doesn't help that every Matrix level looks the same and has the same repetitive music track playing in the background.
Strawman Has a Point: In Dragonfall, the Humanis policlub have propaganda copied straight from 20th century racial supremacy groups, including calling for violence against elves because of an alleged Ancient Conspiracy of elves controlling the world, an obvious reference to anti-Semitic propaganda such as the Protocols of the Elders of Zion. Trouble is, in Dead Man's Switch, you team up with Harlequin, who is part of an Ancient Conspiracy of elves controlling the world.
On the other hand, Harlequin is established to be The Last of His Kind, meaning that the Ancient Conspiracy was indeed true at one point, but it's run out of steam at this point. In a sense, Humanis being fearful of elves for wanting to control Humans is like being afraid of the modern day catholic church out of fear that they'll execute non-believers. It was a legitimate fear at one point, but not anymore. At the end of Dead Man's Switch, Harlequin even has a short monologue on the truth of the matter being a hilariously complicated web of personal agendas and conspiracies all clashing with each other and turning into a giant clusterfuck instead of there being an unambiguously bad single entity at the top keeping the world's evil running on Ontological Inertia. He ends with the assertion that the best way to fight it is to refuse to play into it to begin with, like shadowrunners.