more switches with the FC12, that's mostly it. this allows you to have more functions available at once.
the FC6 has access to the same number of functions/switches (12 switches on 9 layouts, with Tap and Hold for each), but you only "see" 6 at a time, since it has 6 physical switches.
so if you want to be able to select 12 different things (24 really with Tap and Hold) without changing Layouts or Views, the FC12 is the way to go. if you can have "only" 6 different things at any given time (12 with Tap and Hold), then the FC6 can work for you, while taking up less physical space.
again, it's about how many switches/functions are immediately available at once. all functionality is there with the FC6, but you may have to change Views (which changes what the switches do/display) first.
for many users, the FC6 has more than enough capability for what they need to select from at any given moment.