Creating Electronic Binders Using PDF Portfolio - Commenting and Highlighting

For a few years now I have been using Portfolios to create electronic versions of binders. Users want to be able to review, search, highlight and comment within the PDFs - and each have a copy with their comments. Security is also a big deal. My main question is: Is using Adobe Portfolios the best solution for making an electronic binder, or does Adobe or another vendor offer a better one? Recently I saw a product called GDoc Binder that looks promising. For now using the Portfolios is the best solution I know of.
Problems with the current solution: Right now I have to create multiple copies of the document to allow users to comment and highlight on their own copy. File size can be problematic - if it's too big searching can take a long time even after I index the file. Updating and adding sections is problematic since if you update a page or file you could lose their comments, and so I have to update multiple copies of the same file. I know you can export and import comments but that can be complex/time consuming. One question I have: Is there a search and/or report on comments and highlights from the full Portfolio rather than just one at a time?
Since Adobe Pro X I have had to use a custom template from PracticalPDF.com to recreate the list navigation of Adobe Pro 9. I did see another post saying that the use of Flash with Portfolios mean that it's day are numbered. Question: I am curious if this is true, and if Portfolios using Flash are becoming obsolete, what Adobe Pro would use for an alternative?
Thank you in advance for any insight and answers - it is greatly appreciated.

Take a look at the free 'CoolList' layout from Joel Geraci : http://blog.practicalpdf.com/portfolios/

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Creating Electronic Binders Using PDF Portfolio - Commenting and Highlighting

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