Challenges marking scientific papers with the ipad

I have experimented with limited success in using the ipad to mark up and comment upon student work.  With the goal of going paperless with student writing I had them upload research manuscripts in my cell biology class using Dropbox (which worked great).  I then used the Quickoffice HD Pro app to open the uploaded Word documents.  I was quite pleased with the markup options in this program, which allowed multiple ways to comment upon student work.  I was quite bummed that the embedded figures and tables were not displayed using this app, thus making it impossible for me to use this approach for commenting upon student work.  I ended up using Word and a desktop to electronically comment on these assignments.  Next up..exploring ways to mark up pdfs (which should avoid the image issues that I had experienced) and use ical/google cal to set up a calender for reserving access on a departmental microscope students use in my course.