Just wrote up some data on Penguin 2.0:
http://www.seomoz.org/blog/penguin-2-were-you-jarred-and-or-jolted
I just want to add, though, that I'm not speculating about the new ranking factors yet, because we just don't have that information. No one has specifically recovered from Penguin 2.0, and I don't think anyone can tell you exactly what changed.
By the very fact that it's called "Penguin", though, I think it's safe to assume that these new factors are an extension of the old philosophy. I generally back Alan's procedure, because I've talked to reputable SEOs who have had success with it. That success often comes after a hard-fought battle, though. The number of Penguin 1.0 recovery stories that I can document are fairly few.
If you know for a fact you have bad links, you do need to try to remove them first. Disavow can work, but Google needs to see a clear removal effort and it almost always has to be paired with reconsideration, from what I'm seeing. Unfortunately, 2-3 Google reps have given us 2-3 stories on the process, so I'm going by what I've seen work for SEOs who I trust (who have shared details privately, in most cases).