Rich Idiot with No Day Job: Sam might have the most shares of Encom, but he's a college dropout with no job and no social connections outside Alan Bradley and his rescue dog Marv.
Shirtless Scene: The stripping off of his old clothes by Gem and her colleagues. However, judging from how this is a different system from the one in the original film, that might in fact be necessary to get his new attire.
Unskilled, but Strong: He's never seen doing the things that make Users Physical Gods, which is unusual given that he's an accomplished hacker and very tech savvy. He's a good fighter though, and naturally a lot tougher than most programs.
Shout-Out: To Obi-Wan Kenobi in the original trilogy (Episodes IV-VI) of Star Wars with the beard, cloak, hideout, hermit nature, and regret.
Stop Worshipping Me: Subverted. By the time of the film, he's long since accepted that the Programs are gonna worship him, whether he likes it or not.
Coming back from the original TRON, Alan Bradley is revealed to be one of Kevin Flynn's closest friends and still in the employ of ENCOM. According to the ENCOM website, Alan holds the position of Executive Consultant, and later promoted to Chairman of the Board by Sam. He was the man who sent Sam to Flynn's Arcade to investigate a message, starting the search again...
The Chess Master: A mild case of it. In the first film, he'd been building Tron for months beneath the notice of Dillinger and Master Control. The alternate reality game establishes that he's leading the Flynn Lives movement under the name ISOLated Thinker. He's also been minding the store as best he can at Encom for when Sam finally gets his act together, and looking the other way on the stunts. The speech with the pager and the fact he held off until after the prank was likely an attempt at a Batman Gambit, and "The Next Day" shows him going over a Plan with Roy Kleinburg about the company's future without Sam present.
The Mentor: Arguably, since he became Sam's surrogate father during Kevin's disappearance.
Only Sane Man: He's the only one on the board who still believes in Flynn's vision for the company.
The Peter Principle: According to supporting materials including the Alternate Reality Game, he was made CEO of Encom after Kevin's disappearance, and was later forced to resign as a result of the company's decline in the late '80s. Consider that he's a computer programmer, not necessarily a businessman by trade.
Papa Wolf: During the introduction, when the reporters try to swarm the young Sam, we see Alan turn around, looking furious.
Promotion to Parent: Acted as a father figure to Sam Flynn after Kevin's disappearance. But at the start of the movie, their relationship seems to be a bit strained.
Hypercompetent Sidekick: To the Corrupt Corporate Executive Mackey. Also, in the bonus material Flynn Lives, Alan mentions that "the kid earned his place." After all, it must not be easy to rise in a company where your father was publically revealed to be a fraud.
She's Got Legs: To reiterate, there's the scene midway through during the explanation of how Kevin got stuck on the Grid. Whenever it cuts to Quorra, we inexplicably get a full shot that does nothing but emphasize this.
Skilled, but Naïve: She knows her combat skills, but she knows almost nothing about the real world.
Anti-Villain: According to Kevin Flynn, anyway. He's only created the dystopia of the film because that is precisely what he was programmed to do. He simply cannot contemplate Kevin's change in thought.
Also, it is revealed that all he wants is his Creator's approval. In the final battle, he has Kevin Flynn at his mercy but doesn't kill him.
Ascended Extra: From the minor character Clu in TRON. Also in-universe, in that he was a hacker program meant to find things in the ENCOM server in his first incarnation, whereas his second incarnation was one of the three people in charge of the Grid in version two, and eventually the sole leader.
Authority Equals Asskicking: He was created to be a substitute for the Grid's version of God. He takes a direct hit from an Identity Disk without flinching. Pretty much nothing is able to hurt him, let alone kill him.
In a very literal way: Clu has all the authority than Kevin Flynn does, which is why he gets stronger the more Kevin uses his User powers.
Blue and Orange Morality: He acts the way he does because he believes it is how he should fulfill his programs. Bonus points for living in a world where the morality of one is determined by being blue or orange.
Brilliant in that he's yellow, symbolizing how he's just simply good or evil, just trying to fulfill his 'father's' wishes.
Chronic Villainy: He is a program, so he's basically obliged to pursue his quest for perfection, even if it implies genocide.
During the Games, he pits Sam Flynn, and inexperienced user, against Rinzler, aka freaking TRON. As in, the guy who took down Sark, effortlessly crushed four of Clu's Elite Mooks, and helped create the new Grid.
Name's the Same: People forget that this is not the same Clu from the first movie, but a separate program with a completely different function who is named after Flynn's hacking program from the first movie.
Ambiguous Situation / Epileptic Trees: Due to the details of the prequel TRON: Uprising, a strong minority of viewers believe that Rinzler's identity is Beck, the protagonist of that series, instead of Tron as implied in Legacy. The idea stems from the fact that the writers and artists seem to have designed Beck to be what is essentially a non-evil Rinzler in appearance and fighting style, and a major plot point is that he is conditioned to be a replacement Tron.
Badass: This should be empasized: short of Clu, Rinzler is the most fearsome thing on the Grid bar none. Note that during the flashback as Tron, he was able to take out four of Clu's elite Black Guards in roughly the span of 2 minutes without breaking a sweat or even remotely having to strain himself. Compare anyone else who has to tangle with the guards or even some of the higher-level sentries, which usually results in a quick derezzing.
Call Back: "I fight for the Users!", of course. In addition, Rinzler's introduction features him in a four-sided Disc Wars court, just as Tron was introduced fighting a four-on-one game in the original.
Foreshadowing: Two specific examples in Kevin Flynn's flashback to Clu's rebellion. In that flashback, Tron uses two discs at once, just as Rinzler does (they even have a scene where he specifically looks at the discs in his hands as if to highlight this). Secondly, if you listen very carefully straight after the camera pans from Clu smashing the disc onto Tron, you can hear Rinzler's signature sound.
Restraining Bolt: Immediately ceases his attack on Sam when he sees him bleed. Throughout the film, he seems to target everyone but Sam, since his original core program was designed to fight for the Users.