I don't see how the fact that gas planets are capable of migrating inward shows that our model for planetary formation is deeply flawed. I didn't think the current model said that it was impossible for planets to migrate inward.

The point about sampling bias is that our current techniques are bad at spotting systems like ours. If this is true (I think it is, but I'm not qualified to say), we wouldn't expect the evidence to fit our theory even if our theory were true because we are nearly incapable of finding evidence that does fit our theory no matter how much of it there is out there.

Perhaps I mangled that a bit, instead of frost line I should have just said the seemingly most popular theory of how the solar system formed. From the article the bit that caught my eye:

Mike Brown, an astronomer at Caltech, wrote me that while everybody is busy hunting for an Earth-like planet, they missed this story. "Before we ever discovered any [planets outside the solar system] we thought we understood the formation of planetary systems pretty deeply." We had our frost line. We knew how solar systems formed. "It was a really beautiful theory," he says. "And, clearly, thoroughly wrong."

I did some reading into this last year while I was stuck in bed sick and what I came across was it was to do more with light pressure than a frost line. The frostline has more to do with where water is likely to form than how a come to exist.

Light has trouble pushing heavy materials outwards, so theres a denser percentage of them in close to a star, the lighter the material the more it gets pushed out, high percentage of hydrocarbons in outer planets. Like a giant centrifuge. So our system should be fairly standard unless the rules of physics are different elsewhere.

That doesn't exclude random formations as you are dealing with super heated eddies, explosions etc... during formation. Or even stars pulling there planets in. Both our planet set up, and hot Jupiters are to be expected because its a giant chaotic exploding mess.