Part of a conversation between Flynn and Clu reminded me of a coversation between Emperor Marcus Aurelius and his son Commodus in Gladiator.
Flynn was apologizing to Clu for how things worked out, and by extension, how that made Clu evolve into the way he was.
That conversation kinda gave me this impression:
The Emperor telling Commodus how his son's faults were the Emperor's own failings as a father.
I also liked how Flynn's cave dwelling in the grid reminded me of a simpler version of Dave Bowman's house interior at the end of 2001: A Space Odyssey.