What you're planning was part of our South American tour. This is the route we took and comments on the places :-
Buenos Aires. Great city with tons of things to do. We stayed in San Telmo which we loved.
Iguazu Falls. A full day on the Argentinian side and half a day on the Brazilian. This was one of the highlights of our trip and would make our "must see" list.
Pantanal. Great for wildlife (much more to see than in the Amazon) and star filled night skies.
Bonito. Glad we took a detour to have a day snorkelling in the Rio Sucuri.
Death Train from Quijarro to Santa Cruz. An experience we really enjoyed despite it being looooong.
Sucre. A beautiful city and a great place to spend a few days resting and getting a bit of altitude acclimatisation.
Potosi. Astonishing place. A mine tour is a "must do" but you need to be aware of the conditions.
Uyuni. Salar de Uyuni and the altiplano lagunas and volcanoes are a "must see".
San Pedro de Atacama. Nice after the rigours of the salar and altiplano.
Iquique. Nice beachside town. Highlight for us was out in the desert - Humberstone and Santa Laura.
La Paz. Crazy place to build a city, we really liked it.
Puno. Lake Titicaca was a disappointment to us, hugely over commercialised and not particularly scenic or spectacular.
Arequipa. Beautiful city. The Santa Catalina monastery is a "must see"
Colca Canyon. Fantastic hiking. For us this was a "must do"
Cuzco. The city itself is fascinating. Machu Picchu is a definite "must see". Get there early and get tickets for Wayna Picchu.
Nazca. Small aircraft flight over the lines was great.
Lima. Nothing to write home about.
Trujillo. The reason for going was Chan Chan but it's over restored and not that great.
Chiclayo. The Tombes of the Real Sipan museum is good.
Cuenca. Nice city
Alausi. The train down and up the Nariz del Diablo is closed for maintenance, but even if it's open when you go it's only worth stopping if you're going that way anyway. Was one of our biggest disappontments - a bus on rails.
Quito. Interesting city. A visit the basilica is incredible, health and safety is different in South America.
Other places in Argentina , Chile we went to on our trip :-
Ushuaia. Fantastic but a long way from the direction you're going, could be done by flying down and back from BA.
Torres del Paine. Definitely a highlight for us, but again not the way you're headed.
Bariloche. As TdP
Mendoza. Vineyards, great wine and food.
Places we would have liked to go :-
Banos. We went to the hot springs at Chivay in Peru so skipped Banos but would have gone there if we'd had time.