Rondo is physically more gifted than Chris Paul. He is faster, longer and more durable. Rondo is smarter than Chris Paul. He is more aware of what is happening during games and can make adjustments and call plays on the floor like a coach. Chris Paul is much more skilled than Rondo. He's an elite passer, elite scorer, good defender and good rebounder.
Chris Paul is without a doubt the better player. However Rondo has a much higher ceiling. Skill can be learned, but IQ and athleticism can't. Rondo has improved at a much faster rate than Chris Paul. Rondo came into the league very raw as a late round draft pick. Chris Paul was a star from the moment he stepped into the NBA. Rondo has not closed the gap completely, but he's a lot closer to Paul than he was to start. Rondo has also slowly improved his field goal percentage, despite a steady increase in shot attempts, to near 50% and actually shoots more efficiently from the field than Chris Paul. Paul is still the far better scorer because he is a far superior 3 point shooter and converts his free throws.
If Rondo becomes a better shooter, he would surpass Chris Paul as the best point guard in the league. However there is no reason to expect Rondo will become a better shooter overnight. His humongous wingspan and large hands makes it very hard to get a shooting touch. But he WILL improve his shooting, especially as his responsibility shifts from set up man to leader. I have no doubt that in two years Rondo will be equal to if not better than Chris Paul.