Another pass on Legacy and another run through the novelization of Tron proper, and something's bothering me. There's a lot about Kevin Flynn's behavior that adds up more to a case of anti-hero or (come Betrayal and Legacy) something dangerously close to villain. Of course, part of that in Legacy are the writers; Horowitz and Kitiss run entirely on grayscale morality and characters who aren't as clear-cut on the alignment scale as they appear on first pass (just look at OUaT and LOST). That being said, here are the points bothering me about that character.

1) He's established as a guy who has a natural gift for business, programming, and persuading others to do what he wants (Alan and Lora should have been immune to his bullshit, but look how fast he can rope them into a half-dozen felonies), but is otherwise a full-blown Man Child. His primary motivation on the first film is to get revenge on Dillinger for stealing his ideas and a ton of money. Defeating Master Control is the only way he would be able to get back to analog so he could enjoy the credit and cash. Anyone else's concerns could be a second thought at best.

2) Even right before he makes his attempt at Heroic Sacrifice, he kisses Yori, a doppelganger for his ex-girlfriend (and who he knows is happily attached to his new Program best friend). It's very obvious he's using her as a substitute for the gal who got away (who is, from a certain POV, her mother), which kinda adds to the squick.

3) After he does get back to analog, he proceeds to steal his friends' work (Lora's laser, Alan's Program) and conduct highly irregular and dangerous experiments in his arcade's basement, all the while lying to his friends and even his wife about what he's really up to! Seriously, these people are loyal and devoted to him and his cause. Alan keeps the pager for 21 years. Roy loses everything just as he's approaching retirement. He tells them nothing, and leaves them to unanswered questions and guesswork. Repeated digitizations could have done God-knows-what to his DNA (and by extension, Sam's), but he tells Jordan NOTHING. (Tron: Betrayal) And after all this, he thinks so little of his friends and family that he doesn't even trust them with the truth? With an "in case I die or vanish, here's some instructions?"

4) And what is he doing in cyberspace? Millions of sentient, artificial life forms with their own society, goals, thoughts, and feelings, and he explicitly refers to their world as a "game," and "[his] gift to the world," with little if any consideration for them. Clu tells him repeatedly the place has some serious trouble; gridbugs, corruption, drive capacity, but Flynn seems to ignore it until it's literally too late. He also seems to ignore Clu's increasingly brutal behavior, again, until it's way too late. 

5) When the Isos come along, he's so delighted by them that the Programs seem secondary concerns at best. When things inevitably go south on him, he saves Quorra (last Iso), but throws millions of Program lives (including Tron's) under the proverbial bus in the process.

6) Regarding the Isos. Yes, it was a horrible, evil, Sith-Level monstrosity that Clu committed by inciting hatred against them. The creation of Abraxas and cold murder of Radia just scratched the surface. The Iso Wars, bombing of their cities, mass genocide are even worse. However, the Grid was falling apart from gridbugs, system failures, and capacity issues before the coup (Betrayal). It went from being on the verge of irrecoverable crash to stable enough to run uninterrupted for nearly 21 years. The other disturbing element was that Flynn was delighted about the Isos, enough and go on and on about how great Isos were, how much of a "miracle" they were, his "gift to the world." The Programs get slapped with a denigrating label of "Basics," and Flynn doesn't seem to be interested in them (to the point of possibly throwing them all under the bus, Tron included, just to he could save Quorra and his own ass, as noted above). But aren't the Programs also miracles? Aren't they also life from nothing with unknown origin? Aren't they also sentient lifeforms with their own social order, dreams, sense of humor? Weren't they also worth respect? Wouldn't even the simplest accounting script like Ram rewrite everything - science, medicine, religion - just as much as an Iso could? Clu even calls him out on this and there isn't much of a reply.

7) Quorra says he fought against Clu, but there is no evidence of it in TRON: Uprising and his idea of "fighting" in TRON: Evolution was to code up Anon to do battle for him and die to rescue Quorra.

Even worse is that the two other main characters of Legacy are his devoted disciple (who was saved by him while millions of others were left to die or worse) and the son who has desperately wanted to find him, characters who likely have a very large blind spot when it comes to his degree of culpability. I figure that the writers were probably intending a more flattering picture than this, but add up these points, and it doesn't look good for him.

Rebuttal? Additions to the list of disturbing behavior? Something I missed?