You can do most of that from within the PDFMaker plugin for Powerpoint (write bookmarks, include multimedia, etc.) but Reader-extending to allow commenting has to be done in Acrobat Pro once the PDF has been created, and there are some limits when creating links (web URL links can be added in the PPT and will convert across fine, but links to locally-stored files have to be created in the PDF afterwards). However to bring all these features across you cannot 'print' to PDF - you must use the Save As Adobe PDF option, which employs the PDFMaker plugin. This means you're unable to create the "notes" or "handout" views, only the slide deck itself. Speaker notes are applied to the slide as a text annotation (sticky note) on the top left corner - you can't control that but you can turn it off.
PDFMaker will create bookmarks for each slide (using the title) and you can edit them afterwards if necessary. Full text search should work just fine, though it depends on what's on the slide (some 'text' in PPT isn't rendered as text in the final document). Text within the comments (speaker notes) is not included by default when searching, but you can turn it on via the dropdown menu on the search bar in Acrobat and Reader.
If you want more control over the layout of the PDFs and access to more extensive features, then Powerpoint isn't really the way to start. I would advise using a proper DTP package - InDesign, Quark, etc. While PPT can be coaxed into making hardcopies it was never designed for that workflow.
Unfortunately that makes things very difficult. Microsoft doesn't expose the "notes view" page layout to the Save As workflow, it's only created via the print dialog (and if you "print" to PDF you lose everything interactive and get an electronic sheet of paper). PDFMaker only operates via Save As, so it can't therefore include the notes on the bottom of the page, and reimposing the PDF to add them after the creation step is a nightmare of a job.
Gale Miller wrote:
we absolutely must be able to include the notes portion with the slide portion when we convert to PDF.