Previously, I wondered about the defense's competence (especially Knox's lawyers -- apparently Dalla Vedova had never tried a criminal case before!), but now, having read both appeal briefs as well as Massei/Cristiani, I have to take exception to the view you express here. The fact is that the defense put on an extremely strong case; the "woefully substandard job" was the one done by the Massei court in evaluating it.
The testimony of the defense's expert witnesses should have been more than enough to secure acquittal. Francesco Pasquali's experiments should have been the end of the staged-burglary nonsense, and Carlo Torre's analysis the end of the multiple-attacker theory. Even from reading Massei/Cristiani you can tell that Sarah Gino and Adriano Tagliabracci had no trouble pointing out the problems with the knife and bra clasp, as if Comodi's favored "common sense" weren't enough.
Giulia Bongiorno is an excellent lawyer, and Sollecito's appeal brief (which one really gets the sense was written largely by her) shows it. One thing that was really eye-opening was how much stronger the arguments sound coming from the lawyers themselves than coming from journalists reporting on what they said in court -- a discovery which, I have to say, really angered me, because it revealed in retrospect just how poor the reporting on the trial was. The same arguments you heard about are there (including, for example, Bongiorno's famous "Amélie" argument regarding Amanda), but they're much more powerful than what you read in the newspapers.
So when you evaluate how good of a job the defense did in presenting its case during the first trial, you have to take into account that you were hearing about it through the filter of not-particularly-interested-or-competent journalists, on whom important nuances, subtleties, and frankly most details of the arguments are simply lost.