Aside from Acrobat, EagleFiler is the only other app that indexes annotations within PDFs. For me, this feature alone is a major draw for EF. What would make EF perfect is the ability to show these search results within the document in the preview window. For the moment, I would search for the term in EF to pin-point the document. I would then open the document in Acrobat to perform the search again. I don’t have a problem with having to take the extra step except that I don’t use Acrobat to annotate (use Preview) and Acrobat is extremely slow on my system for some reason.
This would be a killer feature for EF in my eyes.