Searching around will find you a treasure trove of advantages, but here's a useful thread for disadvantages and look fors when shifting.
http://www.chiefdelphi.com/forums/sh...d.php?t=109959
Pay attention to the date of the thread. This was before teams had ever used ball shifters in an official FRC match, because they had been released after the 2012 season.
While most information in the thread is general and regards shifting in general, some posts are specific to AM super shifters, which where the COTs shifting gearbox of choice at that point in time.