Hey, I love Central and South America, I've been to eight countries between the two. It sounds like you will primarily be on the east (which is funny, I did the west coast), but here were the highlights for me and you can then figure out which would work with your itinerary.
* San Juan del Sur, Nicaragua...beautiful little beach town, infrastructure in Nicaragua is beyond terrible so it took us forever to get there, but it is stunningly beautiful and very relaxed. I've known other people that have gone there and everybody agrees. Be sure to stock up on "Flor de Cana" rum. At least when I was there, there were government mandated blackouts every night to conserve power, these were really fun and a great way to end up meeting random people.
* Chile. Sounds like you are doing Argentina instead, but I loved everything about Chile. Santiago and Valparaiso are both fantastic cities. Santiago has a huge gay district too. Also, we took the flight out to Easter Island which was expensive and long (5 hours away) but worth it. Unbelievable white wine too, take a wine tour if you're there.
* Panama. Although the boat we got was kind of cheesy, it is cool doing to Panama canal. Bocas del Toro is a beautiful, laid-back beach spot on the East Coast.
* Machu Picchu. I know you said you are avoiding the obvious tourist locations, but this one is popular for a reason. It can get overcrowded, but I've heard the government will be slowing the amount of tourists who can come see it to preserve the site so this may be your last chance.
* Galapagos Islands. I can't even describe how awesome this was. Easily the coolest place I've visited. The wildlife is unreal...swimming with sea lions who play with you, sitting right next to giant tortoises (it felt like sitting with a dinosaur), wading with Galapagos sharks...everything is so unimpressed by your presence and therefore it's so easy to (safely) get up close. Not only that, but the town on the island we stayed was so chill. The locals were beyond friendly, the two (!) bars were so fun and always had a good crowd, the food was fantastic. It is a fairytale spot. To get there you have to take a flight from Ecuador, which is a super cool country in and of itself.
Good luck man, hope you have fun! It is an awesome part of the world.