I got to this thread because I had the exact same problem. I set up my printer wirelessly to connect with an Imac and a Macbook Air, both with Mac OS Mountain Lion. When I asked it to print, there were only a few options. There was no duplex available, nor were there color options. After trying a number of options like reinstalling printer drivers, I finally hit upon a solution.
I connected my printer to my Imac with a usb cable, and it showed up in my system preferences as "Canon MG5400 series -2" I enabled "share this printer on a network." Immediately on my Imac, when I went to print, all the print options were available including duplex and color options.
I then went back to my laptop, and found the options were still NOT available. However, I clicked on the "Printer" line at the top of the Print dialogue box, and it let me choose "Canon MG5400 series -2." As soon as I did that, all the advanced print options appeared on the Laptop Print dialogue box as well.
I don't know if this is the only way to fix the problem, but it certainly worked for me. I know the option that I have repeatedly seen of "Look for a drop-down menu with the heading of either "Layout," "Copies and Pages," or the name of the application you are printing from. Change this to 'Duplex Printing & Margin'" simply does not work, as the "Duplex Printing & Margin, just did not appear.
I hope this works for you as well.
