Off the top of my head, you can't do the following:

• Add Annotations/Redactions/Notes to the PDF. *
• Add additional Pages, Delete or Reorder the PDF. *
• If the PDF is searchable, words will show up when searching but it will not take you directly to that page and highlight them when clicked. (It will only open the document - this applies for office docs as well).
• When viewing them, the entire document is downloaded to your machine instead of just the pages you are currently viewing. (This might be slightly different on web access 10 and Mobile 10). This is especially important when the person viewing it is across a WAN and/or the document sizes are large. 

*Unless exported and changed with Acrobat or another PDF editor.

Keep in mind that all tiff documents can be exported on the fly and very quickly as PDF. If there is a compliance reason why it needs to be in PDF you may want to review this information and find out if exporting is ok. Many systems do allow this. 

For most of our customers the only time we suggest scanning things in as PDF is if they are large color documents with lots of images, mostly because of better compression. That and processes where the document is generated by an outside source as a PDF. (Obviously these sort of things are different from customer to customer).