Hi
My friend and I spent 3 months last year travelling from Rio to Santiago. As it was winter we decided to leave out Patagonia (southern Arg/Chile).
Anyways, must dos in my view are the inca trail, salar d'unuyi, iguasu falls and either the Pantanal (which we did) or the Amazon/Pampas in Bolivia (skipped till next time).
You could go North from Santiago to San Pedro de Attacama do the salt flats into Bolivia then go to Peru/Cusco for the Inca Trail back across to La Paz then go either via Santa Cruz into Brazil and the Pantanal then head for Iguassu then east for Rio or head south again (double back a bit) for Mendoza (Arg) then Buenos Aires if you wanted or straight Iguassu for Rio... We had plenty of time for our trip in 3 months and we spent a week in Rio, BA and La Paz.
What we did was Rio - Ihla Grande - Iguassu Falls - Campo Grande - Pantanal Trip - Corumba - Santa Cruz (Bolivia) - La Paz (4 nights) - Salar d'Unuyi - Potosi (6 days due to strikes) - Sucre - returned to La Paz (4 more nights) - Arequipa (Peru) - Cusco - Inca Trail - Nasca - Tacna - Arica (Chile) - Iquique - Mendoza (Arg) - BA - Salta - Valparaiso (chile) - Santiago
All that in 12 weeks and never rushed either - buses service brilliant, drivers can be like rollercoasters, varies from country to county too though but regular enough, we got one train from Corumba to Santa Cruz - experience i will never forget... we did zig zag a bit but it didnt bother us...
Hope that helps in some way! Very jealous would do it all again in a heartbeat!