Remember that Beck is at the least the sixth apprentice Tron's had. First was Ram, and that poor script de-rezzed halfway through the first movie. There was the Iso, Jalen, who Clu corrupted horribly into a living virus. Then there was Anon, who de-rezzed in a very messy painful way in the Outlands. We also had Dyson and Cyrus. With a track record like that, little wonder Tron is struggling not to get attached.
As far as why Tron gets attached to Beck so quickly? Well, out of all his apprentices, Beck is very much like what he used to be back when Master Control was trying to conquer the digital world. Beck's mechanical skills are also surprisingly close to what Yori's specialty was during those days. Even if the Fanon guesses about Beck being a de facto "son" or "nephew" got Jossed, the similarities are close enough, especially for a world like the Programs', which doesn't have family units in the same way humans do.
This one requires a lot of paying attention to the Expanded Universe. Abel acting as a Parental Substitute, the closeness among the staff in the garage, Paige's mourning for the co-workers that were killed in the medcenter, and even Tron's shock at being betrayed by his fellow security personnel... think about it, Programs do not have the same concept of "family" humans do. Clu was completely baffled about why Kevin Flynn was willing to risk so much for Sam, and the closest Ma3a came to understanding the concept of "father" was "earlier version." Where human society is usually centered around biological family, the Program one is likely centered around the primary function. What family is to a human; the workplace is to a Program.
As seen under Fridge Horror, Dyson may have only been doing what he was programmed to do and viewed Tron as willing to let the system and everyone on it die in order to appease the User. But the brilliance? Remember, Tron wasn't created by Flynn, and Tron was also explicitly designed to run autonomously and make his own judgement as to what was and was not a threat. That's why he was such a grade-A threat to Master Control. Unlike Dyson, his judgement was that the Isos were not a threat. Furthermore, due to his independence, adaptability, and long association with Flynn, Tron's moral outlook was probably much closer to human than most of the other security scripts, which is why they betrayed him.
In the flashbacks to how Tron got his scars, he witnesses the repurposing of his loyal security team, while he is also in a repurposing pod... but never affected. It would have been much safer for Clu to repurpose Tron immediately, and he literally had the man in a repurposing pod. Why didn't he? Because Flynn was the only User to ever interact with the Grid. Every single program in there was created by Flynn, except for the Iso's... and Tron. Coding styles tend to be unique to a programmer, and Flynn and Alan are different enough to likely have very different styles of making programs. Trons code is probably radically different to every single program on the Grid. Clu couldn't immediately repurpose him because he had no idea how Tron worked. In the immediate aftermath of his coup, Clu would have been incredibly busy - securing his position, trying to hunt down Flynn, mass repurposings, genociding the Iso's - he didn't have the time right away to try and figure out how Tron worked. The best solution would have been to hand him over to Dyson for torture, so Tron couldn't escape and could be manually repurposed later. If the show hadn't been cancelled, we might have gotten up to Tron being captured, and Clu fighting to reprogram him while Beck tries (and fails) to reach Tron in time.
This would also explain why Rinzler seems so messed up compared to the repurposed drones. Dealing with completely foreign code, Clu must have had to brute force his way through, leading to him getting the enforcer he wanted, but Rinzler having the broken computer-ish rumbling, the glitchy speech, and interaction with Users being enough to make him snap and take out Clu. Considering the only other example of Clu working with non-Flynn coding turned out Abraxas... Rinzler's general broken-ness was probably the best that Clu could possibly do.
The secondary coloration on the Garage characters makes a lot of sense. Beck's blue highlights? Blue, in that universe, are User loyalists. Beck may not be on Flynn's side directly, but he's on the side of the User-Believer champion. Mara's gold highlights are Gold-Colored Superiority, which makes sense since she is in charge of the garage if Able isn't there or too dead to run it, and seems to be leading an insurgency of her own. Zed's green coloration? Green is a color that isn't associated with User or Administrator, which is appropriate given Zed's True Neutral status for most of the show. And Bhodi's red? Fitting for a Red Shirt.
A major sticking point between Beck and Tron through the series is Tron not being entirely truthful with Beck (first with the true extent of his injuries, and then about Cyrus), which bites them both in the ass. Of course it's justified why Tron would play his cards close to the vest under the circumstances, but it's a bad habit that's not entirely of Tron's own making. Check out the Flynn LivesAlternate Reality Game, TRON: Legacy, and the bonus "The Next Day." Alan Bradley is a master of the Cryptic Conversation, and seems almost incapable of telling the whole truth to anyone, even a close, long-time ally like Roy. Tron, like Clu, got the best and worst of his User.
It's strange that Tesler buys into Pavel's Frame-Up of Paige so easily, she's probably the most loyal of his soldiers... but if he thought that Paige found out that he killed her friends instead of the Isos she helped, she would have a very good reason to betray him, wouldn't she?
Fridge Horror:
It's a Running Gag in fandom about the resemblance between the characterization of Tron in Uprising, and the equally cynical and bitter characterization of Alan in TRON 2.0, doubly so when it comes to their "parenting" style. We know that Programs take on the best and worst aspects of their User. Considering how terrifying Tron can be when he's sufficiently pissed off, it begs the question of what Alan might be capable of if you managed to force the issue. Sure, Alan seems a pretty mellow guy, but Bewarethe Nice Ones.
Somewhere between Horror and Brilliance. If you've ever made the mistake of installing two antiviral programs on your computer, only for one to flag the other as potentially malicious and try to delete it or otherwise completely foul up your machine? Now consider that's exactly what's going on with Tron and Dyson.
It was pointed out on tumblr that the poor fellow who jumped to his death in front of Sam rather than be sent to The Games looked a lot like Zed. Given that we see Bartik die in Legacy, and Zed's chronic lack of luck, that very likely was Zed.
Another "horror mixed with brilliance." Programs tend to be BadLiars, which is completely understandable as they are...well, Programs. The best Tron could manage is lying by omission. The best Able could do is by pointing out that The Renegade's tool was a standard issue and could have been stolen. This makes Tesler so much more terrifying as he was able to lie effectively to Paige, and did so in a way that she would have seen the massacre as her fault for choosing to help the Isos.
After Clu healed Dyson the latter boasted to the captured Tron that he was also made "perfect" by the former, which seems to include a drastic personality change along with repairing the physical damage done by the instigator that head-shot him. While it could be that Clu just gave him a useful upgrade like the ability to track footprints, could it also be that Dyson was partially rectified by Clu while he was "healed?" Not to the extreme as the rest of Tron's team or Cutler, but since Dyson was already unhappy with the Iso situation it probably wouldn't have taken much More than Mind Control to sway him, and his utter disdain and sadism toward Tron seem to come out of nowhere. Maybe Clu wanted a little more assurance that his top enforcer wouldn't pull a coup on him like he did to Flynn? Considering the Super Recognizer was built to rectify entire cities, it's safe to say that Clu's perfect system consists of the removal of free will of every program on the Grid; why should Dyson or anyone else be spared?
True Neutral status for most of the show. And Bhodi's red? Fitting for a Red Shirt.
who jumped to his death in front of Sam rather than be sent to The Games looked a lot like Zed. Given that we see Bartik die in Legacy, and Zed's chronic lack of luck, that very likely was Zed.