The guy said he was trying to establish a world that was both complete and consistent (which is extremely cool and violating a math theorem (Cantor?) that indicates that impossibility). Anyway, he indicates that he has been refining the matrix through an iterative series of approximations, each more stable than the previous. He then pulls a switch from math to Hinduism by telling Neo that he (Neo) is just the latest Neo (the blue boy god, Shiva? Krisna? somebody help me)--there have been many before and that Neo is getting more predictable. Finally, he offers Neo a logical choice--save humanity and lose Trinity or lose Trinity and save humanity. With Star Trek logic, saving the many is better than the saving the one--which Neo violates by choosing the irrational--proving that the Core could still not predict Neo; that the Core had not yet produced a complete and consistent matrix, that Neo's free-will choice could still defeat the machine logic.

Phew!

The coolest hint at who Neo is, came in the last scene: remember it?

Botnst