This is my general answer to people asking for route advice about South America. It's geared towards people looking to spend 5 or 6 months there, but you can tweak it to meet your requirements. Fly from Santiago to Bogota, that would be my advice about how to begin.
Firstly, despite what some people will tell you, 6 months is enough to do this. Granted you won't be seeing everywhere as 'in depth' as you would if you had a year, but it's totally do-able.
I personally wouldn't start in Argentina though. I'd fly into Quito (well, Bogota actually, but you've said you're unsure about Colombia) and work down.
Then my route would go something along the lines of:
Quito - Banos - Puyo - Riobamba - Canoa - Guayaquil Galapagos Guayaquil
Guayaquil - Lima (some people will say to head to Iquitos, which is your choice, but I'm happy enough doing my jungle stuff in Bolivia).
Lima - Nazca (Nazca lines) - Cusco (Inca Trail). See this guide.
Cusco - La Paz. See Bolivia Guide for route details.
Once at Lake Titicaca, head out of Puno to Arequipa, and then on to Chile.
Arequipa - Antacama Desert (Just pick a town)
Desert - Santiago - Conception - Puerto Natales (Extreme South), for the Torres Del Paine National Park.
Puerto Natales - El Carafate, for the Argentinian glaciers.
From there, probably up to Bariloche, then Santa Rosa and Buenos Aires. From here, get the ferry over to Uruguay (Colonia and Montevideo) and then head out up to Foz D'Iguazu to see the falls.
Hey presto, you're in Brazil.
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