I also am having issues with MetaPDF being unresponsive overall. I can’t even scroll through my document in order to read it, let alone make annotations, without it freezing and me needing to “kill” the page. This is the PDF in question: https://drive.google.com/file/d/0BwUWGwdWBhprTE82M3BLSGRiSDA/view?usp=sharing
I find scrolling to be very slow or unresponsive on a 7 page PDF that I am currently on page 5 out of 7 of - I am going through adding highlighting and annotations. I have had to close and reopen it a few times. I’d say I’ve highlighted about 60% of the words on each page and have an average of one annotation per page.
Highlighting is now slow; typing comments is slow; scrolling is slow etc. It becomes unbearably slow and completely stalls - when I need to scroll sometimes I need to close and reopen. Typing comments takes patience.
I note that this thread is about two years old now so I really hope the speed problem will be sorted soon as I’d like to keep using MetaPDF if possible. I appreciate that it is in Beta, but, at this rate, it might just take me too long to do my work in it.
Also, any file that I let sitting open while I do something in a new tab for a few minutes generally needs to be closed and reopened before continuing to use it.
I don’t think that this is specific to this PDF, but rather to do with the time I’ve spent on the page and the amount that I’ve marked up the document… Can’t be sure though!
Thanks for all your work on MetaPDF.
I had just about finished going through my 7 page PDF (which had been opened and closed several times, successfully saving my annotations etc.), when it froze during a long annotation. I had to close and reopen, and now all of my highlights and annotations are gone. 
This is clearly far from ideal.
I experience similar issues with overall slowness on some PDFs.