I have the same problem, but there is a twist: on my Thunderbolt Display or built-in retina display (MacBook Retina, Early 2013), scrolling w/ PDFs is *completely* smooth.
On my Dell display, connected via HDMI, it is *completely* unusable (exactly as described by others, above).
Clearly, this is a display driver issue, related to something that Evernote is using to render embedded PDFs (i.e. NOT viewed as attachments).
It would be super great, as a work-around, to be able to toggle on/off ALL PDFs to in a note as attachments or in-line, so I could at least get back to work.