It would be interesting to read the Nature paper, as this articles doesn't go into any details.
...Jupiter and Saturn then became immersed in a disk of thousands of tiny balls of rock and ice, known as planetissimals.
The combined gravitational effects of these balls, which lay in a disk beyond Neptune, caused the position of the planets to migrate...
If they're beyond the orbit of Neptune, then why are only Jupiter and Saturn immersed? I imagine there would have to be a lot more than "thousands" of them to explain any significant migration of the gas giants.
...Saturn moved slightly away from the Sun, while Jupiter moved slightly towards it. This process eventually resulted in Saturn having an orbital period that was exactly twice that of Jupiter's...
But Saturn has a period of ~33 years, and Jupiter has a period of ~12 years. That's not 2:1. Or did Saturn continue to migrate beyond the Jupiter's 2:1 exterior resonance zone, in which case, what's the relavance of that sentence to this article?
To expand upon this a little, I believe the reason that Jupiter would migrate in, and Saturn migrate out has to do with Jupiter's greater ability to eject things from the solar system. As Jupiter or Saturn gravitationally perturb an object into a higher orbit, they must migrate inward. And if they perturb something inward, they must migrate outward. Objects that get perturbed still have a Jupiter or Saturn crossing perihelion or aphelion, and ultimately return to get perturbed again. The net bias is 0 minus the bias from any object that gets ejected from the solar system, never to return to get re-perturbed again. Jupiter has only one way of ejecting objects, so it migrates in. Saturn has two ways of ejecting objects: do it itself, or perturb it inward and let Jupiter eject it. Since Jupiter is much more massive than Saturn, the latter is far more efficient. So Saturn, with a net bias of perturbing objects inward, migrates outward. Uranus and Neptune also have a net bias that causes their orbits to expand. And Jupiter with a net bias of perturbing objects outward, migrates inward.
His results suggest that the giant planets' obliquities might have been fixed into their present-day positions by gravitational interactions between the planets during this migration.
How? I wish the article elaborated a little more on this. The Nature article should explain it. I'll have to look at it the next time I'm in the library.