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.
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.
Demonic Spiders: 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.
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.
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.
Game Breaker: 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. With this skill, you can practically keep firing your pistol for any round you want as you do not have to spend an obligatory AP to reload and makes magazine capacity an afterthought; only the damage inflicted per round is made important. 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. But only on pistols/revolvers; the other guns have no such luxury.
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.
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.
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.