I have an Africa Twin (after 10 years of Transalps) and use it for the daily commute (150 miles a day). It's very reliable, but the build quality is not as good as people generally believe (mine is a 2001 model). You may not be worried by rust though!
Knowing parts (but not all) of South America I'd say the AT would be fine for most things (I saw quite a few out there), but it would not be my choice - in fact the Transalp is a far better bet, and there are more of them too. The AT is just too heavy, and the trans-continental cruising ability of the AT and the BMWs for me somehow detracts from the journey, because when I travel I like to see and spend time in the areas I'm travelling through rather than get through them ASAP. These larger bikes tend to encourage that, at least with me aboard!
Overall, I agree with Grant et al. - a 650 single is the way to go. Keep it light and simple. If you are not two up or carrying the kitchen sink a single is enough, liquid or air cooled. Any bike will do though. Perhaps you need to have a shot at a shorter but similar trip with an AT or GS to find out what you'll want.
Tall men see everyone else's bald patch but their own.......