Yeah it's a tough one. Because you can almost take any route you like. I'll give you some of my highlights. I zig zagged a fair bit.

Bolivia: ruta de las lagunas, salt flats (in uyuni) Sucre (really nice town, could have stayed longer, cheaper Spanish lessons in south America) Cochabamba (it worth it just for the road from Sucre and Potosí) Villa tunari (over the hill from Cochabamba, into the jungle) route 25 from Cochabamba to Coroico (ask about the water level of the river first) death road near Coroico (not that good but it's a must do) La Paz (just to get some good burgers and ) Copacabana (really liked it, much nicer than Puno on the Peruvian side)

Peru: Perú is huge, get ready for some long stretches of "not much". Entering from copacabana go through Puno and down to Arequipa, (after Arequipa and before Cusco you have the option of dropping to the coast for Nazca and Huacachina, personally I don't recommend) Cotahuasi, Colca canyon, Cusco (lots around here, rainbow mountain, Choquequirao, Machu Picchu etc) after Cusco head north staying in the andes, Huancayo, Huaraz etc. Before crossing to Ecuador I'd recommend popping to the coast, lobitos, Mancora.

Ecuador (you didn't ask but still) it's small enough you can do a good loop. Over to Vilcabamba, baños, Quilatoa, over to the coast a bit, puerto Viejo, back to Quito, up to Colombia (I liked the San Martín crossing over towards the jungle)

Colombia is also big, but if you zoom in on the map, a lot is jungle or not accessible. So some highlights would be San Agustín, Cali, Salento, Bogotá. I need to spend more time there and don't have much more info but I will update you in a few months!

All I do is chuck all those pins into a map and a route will show itself. As you travel other people will give you more places to add to it. I wouldn't worry too much about having a very fixed route.