Not only is Paul better than Rondo, I think he's significantly so. Rondo is a top five PG, but there's still a large gap between the two players. I expect there will be until Rondo becomes a competent shooter on his jumper and free throws. Paul is also more consistent in terms of bringing his "A" game.
But what if you put Rondo on a team without the big three so he's more of a focal point of the offense? If he's getting 18-19 points and 11 or so assists and Paul's getting 21/11 with Rondo still playing great defense and rebounding well is it still a significant gap? Also, it's a lot easier to appear to bring your "A" game more often if you're the focus of the offense every night.
Paul's a better free throw shooter, which is important. But while he's clearly a better outside shooter Rondo seems to be much better at getting to the hoop. One stretches the floor, but the other can be devastating, as the Cavs will tell you.
There are a few things we know about the NBA. If the overall talent level of the team goes down, player's numbers often go up. It's the "hey, someone's gotta score" theory. So yes, Rondo's scoring numbers may go up in the future, as he generates more of the offense himself. That doesn't mean he will be as good as CP3, even if his counting numbers improve. I'm pretty sure the advanced stats (which I don't completely understand, get into, or care all that much about) will continue to favor CP3 (assuming they currently do, as I don't really know).
I agree with Roy on this one. Rondo is top-5, CP3 his higher top-5, and not all top-5's are equal.