At first, when Arpeggio shows that he didn't use Clockwerk's brain for anything, you think he just had it to have it. But, when you realize that Clockwerk never came back online, you wonder why? The answer, Arpeggio tampered with the brain so that he could make his evil scheme work.
Or he never turned it on. Since Clockwerk didn't activate when Neyla entered him, it's possible Arpeggio kept his brain off and prevented him from awakening fully so that Clockwerk didn't do anything. Who knows what would've happened if he had it on and Clockwerk woke up.
Or maybe he never even installed the brain. For all we know, it might still be out there...unaffected by the destruction of the Hate Chip...
The latter is unlikely, considering every part of Clockwerk rotted when the Chip was destroyed. However, even though Neyla got steadily more aggressive as the story went on, by the time the gang manages to crash her in Paris she has went completely psycho. It may be possible that Clockwerk's sheer hatred affected her.
Based on the fridge horror below, Clockwerk is shown in the background watching the character. Now the reason he doesn't attack Sly or his ancestor is probably cause he may not understand what's going on, why is there another Cooper here in the timeline and how is it he knows the current Coopers' moves and others he didn't know of based on the time period. So instead of attacking him, he's spying on them to discover their strengths and weaknesses so he can formulate a plan of attack. Really adds into the Paranoia Fuel.
In the first game, each member of the Fiendish Five had a preference regarding the various parts of the Thevious Raccoonus:
Sir Raleigh, which is a frog, has the Ninja Spire Jump.
Muggshot the gangster has the Rail Walk/Slide, which was developed by "Tennessee Kid" Cooper.
Mz. Ruby, the witch who deals with zombies and ghosts, has the Invisibility.
The PandaKing has the pages written by Otto Van Cooper... including how to fit a heavy machine gun on a vehicle, among other things.
Clockwerk is the only one who doesn't keep any part of the Thevious Raccoonus (usable in the game, anyway) in his levels. Probably couldn't stand to have something "so Cooper" near him.
However, he did create the "owl dialect" that prevented Sly from getting the Game BreakerTime Stop right away and use it against him. You can never be too careful...
Toothpick wears his Sheriff's badge on the wrong side of his chest.
Why is Ms. Decibel attracted toLe Paradox? She has a trumpet stuck up her trunk, so she probably has little, if any, sense of smell.
During some of the hacking segments in Thieves In Time, you can occasionally hear an electronic voice saying stuff like "What are you doing, Bentley?" Knowing that Penelope was working for Le Paradox and is a tech whiz on par with Bentley, isn't it possible that she designed the firewalls and security features on the computers to recognize Bentley's hacking style?
In Honor Among Thieves, Sly's Father is shown to display some hints of being a Gadgeteer Genius. Dr. M, supposedly being the smart one of their group, may have felt like he wasn't needed due to this, sparking argument among them and eventually leading to their separation.
Bentley's increasing Moral Dissonance in Sly 3 may be attributed to his condition and feelings of inferiority towards Sly. His escapades throughout the course of Sly 2 boosted his self-confidence, only for it all to come crashing down on him at the very end. Frustrated by this, he proceeds to devise plans that show he's no push-over. The events in Venice only cemented this issue, getting pushed around by Octavio. And then he finds someone of like mind, only for her to fall for Sly. He even has Sly sit out on jobs that he could pull off easily in episode 4, leaving the raccoon a bit confused.
In Sly 2, Murray has to disguise himself as a moose guard in order to get some information from the other guards. He accomplishes this by wearing a taxidermied moose head. A taxidermied moose head that looks exactly like the not-dead guards. In his Let's Play, Kite Ryagara meditates on this briefly before coming to the conclusion that lumberjacks are snooker loopy.
Episode 7 of Sly 2 has a mission that calls upon Sly's pickpocketing skills to retrieve dental radio transmitters from sleeping bears (while they're yawning). How does he do such a delicate task with a huge cane, and such that he doesn't wake the bears?
Sly 2 Episode 1 first pickpocket mission. In order to access the spotlight guns room you have to pick pocket 6 special fragile keys, to slow down the ceiling fans. Being as not many thieves would even think to use the fans to get to the chandelier, one has to wonder how much trouble is it really worth to make sure no one touches your thermostat?
The gang's treatment of the guards; they see them as nothing more than bait or sacrifices. What's worse is you actually having conversations with guards in Sly 2 and 3, and seeing a more personal side to them (for instance, one of the guards in the Venice level talks about his mother's spaghetti sauce). So you're essentially slaughtering dozens each level.
Well, your main weapon is a cane. Not a particularly lethal weapon. So it's possible they're just KOed, for the most part.. Also, a certain level of Cartoon Physics applies. It doesn't apply everywhere, but helps assuage some of the guilt.
In Sly 2, Neyla claims that the amount of guard casualties during a heist that happened offscreen implies that it wasn't the Cooper gang (and Carmelita, who knows the Coopers, doesn't contradict her on that), so presumably the guards that get taken out on-screen aren't dead, excluding the explicitly fatal (feeding them to a crocodile in Sly 3, for example). Of the three main characters, Sly uses a cane, Murray uses his fists, and Bentley uses sleeping darts that can be backed up by bombs (and, in Sly 3, he can attack with wheels). So Bentley alone has a particularly fatal weapon (that is, it's hard to believe that drugging someone to sleep and then bombing them is 'just a KO'. Given Murray's strength, he could probably murder something barehanded, but equally plausible that he can just knock them out for a bit.), but the option is the Player's whether or not to use it. The disappearance of guards is a simplification of the Non-Lethal K.O. — if the guards you dealt with woke up eventually, every time you knocked them out, it would make the game a lot harder, especially since it would be theoretically possible for the guards to rouse their clonked-out companions. Or I'm thinking about this way too hard.
So, basically, yes, the Cooper gang are unrepentant murderers, but they're not blazing a bloody path across the world, especially since the idea is "don't get caught so you don't have to deal with the guards in the first place". And most of the people they deal with are in crooked employ to begin with — if they were killing innocent civilians, I HIGHLY doubt Carmelita would be nearly so lenient towards Sly.
In the 6th world of Sly 2, the gang has to jump onto trains (or Iron Horses) to steal the Clockwerk Stomach and lungs. How exactly do they get off of the trains? Jumping off of trains moving that fast probably isn't exactly safe, even if they're jumping into something soft like snow. The train would probably stop eventually due to the removal of its power source, but by then guards would probably be checking to see what's wrong, and there's not exactly a ton of places to hide on the train. Also, if the length of time that they're on the train is any indication, they're quite far from the main village where the safe house is, so it'd be a long walk back, especially considering how cold it is.
In the Ice Age stage of Sly 4, two of the mammoth guards mention how a former guard named "Joe" was skinned as a present for Le Paradox for offending The Grizz. Later on, Sly dons a Sabertooth tiger skin as that level's costume. While that is Fridge Horror in itself, was that skin Joe?
In Rioichi's Sushi House in Sly 4, there are murals depicting Rioichi's friendship with a shark he let free once he managed to catch him. Years pass and the shark lets Rioichi use his body as sushi to open his restaurant with...
Clockwerk's cameos in Sly 4. You can see him and his robo-falcons perched along the various levels. It's really easy (and scary) to say that you may have been playing as the ancestors right before their deaths at the hands of Clockwerk as they finally go back to their respective timelines at the end of the game.
Even creepier if you discover him relatively close to where you begin a mission or where you were looking for collectibles. Such as in Mice and Mechs, where he is perched on the clock tower. Meaning if you happened to be exploring that tower, he was right on top of you the whole time.
Made yet more creepy by the fact that Clockwerk basically knows about Sly's time-traveling now and just happens to be wherever he goes. The setup for the plot of Sly 5 anyone?
Here's a REAL creep factor for you: How can Clockwerk be fully robotic during time periods when advanced cybernetics hadn't been INVENTED, yet...unless this is the PRESENT Clockwerk, somehow back from the dead and following Sly and his friends through time?
Or perhaps he invented them himself. If Clockwerk had a mechanical body before most people had machines that complex, it suddenly becomes horribly clear how he managed to hunt down the Coopers so successfully until Sly's time. How could any of them anticipate a metal bird being alive, much less find a way to fight it off when it came for them?
Seems like they're just easter eggs and never really are "canon" in a sense, since especially you can find a piece of his eye.
Unless they aren't the original Clockwerk, just some knockoff (or knockoffs?) someone made from scratch to stalk Sly's gang, since they appear much smaller than he did.
Remember back in the first game where you had to run away from the giant serpent-like beast from Mz. Ruby's stage? Remember how Sly hinted that Mz. Ruby was more concerned about keeping this beast in instead of keeping intruders out? Remember how you wound up setting this beast free in order to progress through Mz. Ruby's stage? Where the hell did it go afterwards? Did it swim back to its lair, or is it still roaming around the swamps of Haiti because you released it?