It all depends on what you want to do with Evernote.
If you mainly want to upload your annotations to Evernote to work/view with other apps in your PC, tablet/phone/ipad, Evernote uploads from Reader can be very useful.
If you often create web page notes using Evernote Clearly and want to read them later with Reader, using Evernote with Reader would be an advantage.
I do both. I write reports based on all annotations I upload to Evernote and apply them to Word docs later. I make web page clips, mainly news articles and reviews, using Evernote Clearly and then sync with Reader later for hours of reading.