Flynn, the lead hero of Tron, becoming the villain (as CLU,) and sacrificing himself to stop "himself," may have been an old story. (Or may not.) But it was a less commonly used old story than Tron's, which was basically, hero beats bad guy.
I'd say the original and sequel both share the same story: antagonist in a strange land succeeds through the superiority of his ways.
A very European idea.