The reasons ctOS has nothing on Aiden are either he hacked it or his outfit: his hat and neck gaiter screw up ctOS' facial recognition.
It seems more than likely that he hacked it, every time you view him from a camera his entire body is pixelated except for the sequence where he is in jail, and during those times it identifies him as "Joe Smith".
It's revealed in the book Dark Clouds that the phone itself has a program that distorts just the person holding it.
There is a camera in Nicky's house that ids him as Aiden Pearce, but it registers an error for his age, occupation, and details. I just assumed it was tied to a facial recognition error. In Nicky's house he never wore his full face covering gear.
Aiden can track pretty much any human being with an electronic device, explode city streets with reckless abandon, and even shut down an old man's pacemaker, but he can't call Clara to let her know she doesn't have to die to save his sister?
She didn't pick up because she figured he was angry at him. Or she put her phone on silent because she was going to a cemetery. Also, she wasn't planning to die, she was just going to put flowers on the grave, and got ambushed.
It doesn't occur to Aiden that Clara would still be trying to make amends after her role in Lena's death was exposed, and the time between Aiden getting Nicky out of Chicago and storming the Merlaut is presumably, about how long ittakes to drive from the Motel in Pawnee to the Merlaut, so, since he hasn't heard from Clara since Default's attack, he doesn't think to update her.
The Karma Meter will fluctuate even if you do things that no one should ever suspect you of (like hacking a conduit to burst when you're innocuously standing off to the side.
How on Earth can Nicky not know Aiden is the vigilante? They say his full name in radio broadcasts and his name isn't exactly common.
Story-wise they actually only start saying Aiden's name after she gets kidnapped, so she wouldn't have heard those broadcasts. However broadcasts relating to Aiden's reputation can be heard anytime, which is likely an oversight/expectation by Ubisoft that the player wouldn't have maxed out their reputation bar to hear them before Act 1. Or maybe Nicky just doesn't watch the news.
One of the popular complaints about the game is that the driving physics are very flawed. I noticed that, at least in some cars, there are manual transmissions. It only just occurred to me the other day: Maybe the handling is so terrible because Aiden doesn't know how to drive a stick-shift.
Another possible explanation: the game takes place in Chicago which isn't exactly known to have good drivers. In fact every so often you'll see one car ram into another at a stoplight even without hacking it.
Aiden's overprotective behavior makes sense when you look at his backstory, His family fled Ireland to get away from his abusive father. Many kids in abusive homes tend to gain complexes when they get older, some become abusers themselves, Aiden however, became protective of what family he has, to the point of vengeful if even one of them is harmed.
Much of the game's backstory revolves around blackmail. So when Aiden decides to blackmail Bedbug to get him to infiltrate Rossi-Fremont, it shows he really is Not So Different from the people he's fighting against.
At the very end, Maurice is mumbling "1,2,3,5" to himself. What is this? It's part of the number. The Fibonacci numbers are also shown around the victims of Serial Killer. In one of the recording sets you can pick up, it's explained that the Belwether "crowd control" program was tested by issuing the Fibonacci numbers out and maniplulating people to respond back with it.
Why all the family drama around Aiden's sister (and her kids) specifically? Because this game is full of troublesome Big Brothers.
It's derided as an unrealistic move that everything is hooked into ctOS - Who would do that kind of thing? We would - The ctOS is a refined version of the 'Internet of Things' and the game does a wonderful job exaggerating the real-world security problems caused by common everyday devices having internet connections, especially since those connections are often insecure wireless ones.
Some of the things about ctOS ingame may or may not be really happening IRL in Chicago. The cameras? They exist, called PODS, and monitor their areas 24/7. Private cameras are also hooked into the POD system. If Chicago keeps going, ctOS may become a reality, which also drives this into Fridge Horror, since there could be a real-life Watch_Dogs going on if that happens.
In an Ubisoft blog post the PODS were implied to be the reason why the game was set in Chicago. Aside from the cameras, predictive policing using aggregated data processed by computers is also a thing in Chicago (Incidentally predictive policing is a topic in Watch Dogs 2). In an interview with Polygon Thomas Geffroyd, Ubisoft's content director said: "...We feel [the game exists] in the present, in the now."
During the end of the game, Clara dies, and immediately afterward Aiden is in Focus mode unloading on the attackers. If he'd reacted sooner, he would've prevented it, but could he actually have reacted sooner? In gameplay, Focus mode needs to be turned on-and-off, and he's specifically stated to have picked it up playing chess, which often has similar 'focus' in thinking/planning of moves. So basically, Aiden does not have those reflexes all the time; he literally has to go into that special state-of-mind to do so.
There are three ways you can think about Aiden's lack of personality: either the writers were lazy, or he is a Vanilla Protagonist, or he is camouflaging himself. Keep in mind he wants to have no identity anywhere so he could be deliberately keeping himself as plain as possible so there is nothing that can be picked up about him. By contrast, the civilian's profiles are filled with little titbits and trivia about their lives and personalities (read more about it here). It is their different personalities that makes them unique and they form a huge part of their identity both in real life and in the digital world. In other words, Aiden might be deliberately suppressing his personality to hide in plain sight as only 'characterless' people like him get to live unnoticed by ctOS for so long. We need to have a personality to have individualism and an identity after all.
Aiden hacking Quinn's pacemaker in the ending isn't nearly as out there as one might think. As is the case in real life, it's set up with a Body Area Network so it can be easily adjusted and Quinn's medical files can be updated more easily. It's facilitated by a standard that allows network and even internet access should remote observation be considered necessary. Quinn's pacemaker would still have internet access enabled, as surgery was recent, meaning Quinn would still be under remote observation by medical staff. (Assuming he didn't outright request such.) Hence Aiden giving him a rather fatal surprise.
Dotted about the Bunker you can find audio logs detailing a contest of rather cruel and inventive pranks between Ray and Tobias, the final one, one of Ray's, implies the contest would continue but no other audio logs can be found. Why? It is likely that the prank actually came fairly close to the point that Ray was fired, so the contest was dropped, particularly as Tobias dropped off the map not long after according to other audio logs.
Quinn has a failing heart, which is kept alive by a pacemaker connected to ctOS. Now you have a good reason not to visit hospitals.
Possibly, Quinn was a wealthy and well known individual, someone probably hooked his Pacemaker to the wireless in order to blackmail and threaten him into doing what they wanted. Now that people with a similar idea could be doing the same to other individuals around Chicago, or since ctOs is branching out, across the US.
Not necessarily. Some pacemakers are designed with limited digital input for non-invasive interfacing. My uncle's doctor, when his pacemaker was messing about, had it recalibrated by sending a signal down the phoneline. Not via Wi-Fi - by placing the handset to the pacemaker. Aiden could've shut down Quinn's pacemaker using any mobile, even the old brick phones!
Actually, what's going on with Quinn's is more and more the standard (I go into specifics above), though usually internet interfacing is disabled, leaving only the short range BAN. However, someone of Quinn's stature would likely have had it enabled for remote monitoring purposes in case of emergency. And, if I might add some more fuel to your nightmares, this is in fact a real-world concern.
The perpetrator in some of the crime missions yells "Robots Everywhere!" It seems as though he's playing the Alone Digital Trip.
And not very well at that. Aiden's The Stoic, but somebody else could suffer some serious trauma from failing that.
Speaking of the Alone digital trip, pay attention to the voiceover, it's Nicky's voice viciously attacking Aiden, including saying You Should Have Died Instead in regards to the accident that killed Lena. Why would Emperor Rat have put that in? He didn't. Remember, these are, in effect, drug trips, dredging up stuff from Aiden's mind, it may be Nicky's voice, but these are things Aiden are thinking.
It can be considered mildly surprising that Charlotte Gardener is a front runner to replace Rushmore after his death, given that there were already a lot of people protesting ctOS and, if one intercepted call is to be believed, seeing her as a lying witch. Particularly after Damien's rampage, Blume can try to spin it people will have figured out that ctOS was partially to blame. So why would Charlotte be a popular choice for mayor? Bellwether.
More chillingly, was this Blume jumping on an opportunity... or did they create it? We already know they used Bellwether not just to rig elections, but to directly manipulate Rushmore and Rose into getting together, and presumably they had a hand in pushing them towards the argument that killed her. Whose to say some of the events that led to Aiden releasing Iraq's blackmail wasn't the result of Bellwether suggestions... whose to say that all of it, all the way back to the Merlaut job, wasn't?