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From a simple feature perspective Goodreader includes a crop capability that doesn't seem to be available in iAnnotate. This makes it particularly easy to arrange for viewing a PDF by cropping on the fly. This together with scroll-lock (which both have) is really helpful.
From a subjective point-of-view I find the iAnnotate controls obtrusive and overbearing. I much prefer the controls approach with Goodreader.
I do think that the Preview view in iAnnotate is helpful whereas in Goodreader there is a preview for only a selected PDF in iAnnotate one does see a grid of preview thumbnails.
I also like the tabbed presentation of multiple open PDFs in iAnnotate which is not available as such in Goodreader - although switching between PDFs is pretty much just as easy and current settings and position are recalled for each PDF.
I have not tested the current iAnnotate annotations but I recall that one problem was that they were not readable in Adobe Reader / Acrobat making it sort of a problem to move PDFs between systems with annotations in place.
So I was perhaps engaging in hyperbolé but I would say that I much prefer Goodreader and since the addition of annotations I have no need or interest in continuing to maintain iAnnotate on my iPad.
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