Some changes I would have made...
- Greta Lee's character Eve should not have been the CEO; just make her a random hacker or lowly computer whiz working at ENCOM who is obsessed with Sam Flynn & the Flynn family legacy.
- After Legacy, Sam worked on the permanence code w/ Quorra but realized the implications it'd have on the real world so he stepped away... not thinking humanity was ready for such technology. Eve finds him in Antarctica, living off-grid.
- No separate Dillinger company; after Sam Flynn disappeared from public life, Ed Dillinger Jr. (Cillian Murphy) usurped control.
- Eve thinks her day job is creating elements for a new video game for ENCOM, but those programs are actually being used by Dillinger to sell to the military.
- RECAST Jared Leto... Keanu Reeves, Dave Bautista, Rami Malek, Andrew Koji, whoever. It's just a cypher character but certainly we could do better.
Hell, you could do a lot of the stuff that you want by just changing all of the character’s roles slightly and reworking some plot details.
Keep Sam Flynn as CEO of ENCOM, and have Ed Dillinger, Jr. selling his software to the military under the guise of training simulators for soldiers to prepare for field combat, but in actuality they are being used to gather years and years of combat data for the programs contained within to use against any opposition when they invade the real world to take over. However, he requires the permanence code Sam and Quorra were developing, as the programs can only last in the real world for 29 minutes at a time. You could use both of those reasons as an in-universe explanation for why it has taken so long for Dillinger, Jr. and the MCP to enact their plans.
Greta Lee’s character, after figuring out Ed Dillinger Jr.’s plans, brings this Sam and Quorra’s attention. Not wanting to directly intervene as it would raise Dillinger, Jr.’s suspicions, they direct her to Julian Dillinger, the black sheep of the Dillinger family, who saw his father for who he was and went against him (which is why he was never mentioned or brought up in Legacy). She finds him in Antarctica where he’s been working behind the scenes to create his own rival MCP, which he names Ares, to counter and fight against his older brother’s program. By the end of the movie, you could have the original Tron, who is looking for a successor, hand his role and title over to Ares, maybe due to the previous reprogramming by Clu 2.0 causing him to slowly degrade (let’s face it, Bruce Boxleitner ain’t a spring chicken anymore and isn’t gonna be around forever), because, no matter who it is, the world will always need a Tron. Plus, you can’t put Tron in the title and not have Tron.
I like the idea of Sam and Quorra having a kid (preferably a daughter, since the the first two films each had a male protagonist and it would be nice to have a little change up) as our viewpoint character and way into the film and to draw new and younger audiences. Have her DNA, being a human/ISO hybrid, be the key and solution to the permanent code problem, and a good portion of the film is a race for our main characters to get to her before the main villains do.
Just my .02.