In the final scenes of Legacy, there's an event horizon, so to speak, where Kevin Flynn extends his arms toward CLU and says honestly, "I'm sorry."
He's sorry for the way things turned out, sorry for not achieving the "perfection" that drove him to create CLU, quite literally in the first place. It's the only moment I know of, in film or books, or especially in real life, where the Creator of a world offers an apology to his self-aware creation. Not only that, but this deity explains himself: "The thing about perfection is that it's unknowable. It's impossible, but it's also right in front of us, all the time. You wouldn't know that because I didn't, when I created you." Imagine hearing that on Sunday.
That scene is one of many in Legacy, I think, that are subtle and yet as deep as your philosophy professor would love. The earlier shot of the female program sinking to her knees, hands clasped in worship as both Flynns exit the EOL club really sells the Creator role, too. However, if the day comes when some bearded old dude knocks on my door and says he created me and that he's sorry it didn't turn out so well, that he's sorry for making me ginger, I won't think twice before reacting exactly as CLU did.
