Which nature-based South American trip would you recommend?

Haven’t been to Amazon but Galapagos was phenomenal. I liked that over Patagonia or Iguazu

Patagonia and it’s not close

If I can swing it, I will try to work remote from Chile for a month and use weekends and some PTO to do things like the Atacama desert, one of the lake towns, and likely Torres del Paine over the course of 5 weeks.

From your list, for wildlife:

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2. Amazon trip via Peru

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There are some good lodges several miles up and down the Amazon river from Iquitos, and they have very good guides. The lodges are in the middle of pristine forest. This has the largest diversity of life, though not necessarily the easiest to see. The rainforest can be surprisingly quiet.
But there usually are monkeys around the lodges. Lex Fridman recently did a podcast from the Peruvian amazon basin that is quite good (4 hours long).

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3. Galápagos Islands

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- This has the most wildlife of any trip to South America, and it's pretty tame and you can get close. But not as much variety as other places. No monkeys, sloths, caymans. But the birds are everywhere (not a lot of species, though). Saltwater Iguanas, tortoises, turtles (great place to snorkel), seals, flightless cormorants, penguins. It's a fun trip.

Haven't been to Brazilian Amazon, there probably are places similar to Peruvian Amazon. A cool trip is the Brazilian Pantanal. Jaguar is pretty much guaranteed, giant anteaters, cool birds (Hyacinth Macaws and Jabiru are great there). There is a lodge where Ocelots come in at night to eat chicken they put out.

A stay at the Canopy Tower in Panama can be very good. It's a remodeled US radar tower in the canal zone. Monkeys and sloths are right outside the window. Excellent habitat because the canal zone was never developed so it's pristine. Pipeline road nearby is a near legendary birding spot.

Ecuador - both slopes out of Quito, within a few hours. There are nice lodges that can arrange things. The advantage is it is cooler than the others due to the elevation. It's my favorite birding in the world. Lots of colorful birds, and other good stuff is possible, monkeys are likely at lower elevations.

It's the easiest, by far. Direct flight to Panama City on Copa. The lodge picks you up at the airport, and takes care of everything. They have several very good to excellent guides. Somewhat geared to birding, but there was a group there looking only for monkeys and sloths. A couple of friends went recently on my recommendation and loved it. It's the easiest way to get started on wildlife of Central and South America imo, and honestly the wildlife and birds matched or exceeded my Costa Rica trips..

I've done most of those things and enjoyed them.

I was just at the Galapagos in April and it was phenomenal. Most of the amazing stuff about the islands, though, is underwater. Snorkeling at Los Tuneles on Isabela and seeing seahorses and a penguin was cool, but spending time with a dozen huge turtles (getting a foot away) was amazing. Diving at Kicker Rock was one of the greatest travel experiences of my life (and I've been to 43 countries), but I know that the snorkelers on that trip had a great time as well.

Hiking in Argentine Patagonia (El Chalten) in 2020 was some of the best hiking I've ever done, and the Perito Moreno glacier is very much worth it. I did not really enjoy Bariloche, but I was there in March and it was dusty and dry. In Chile, I never made it south to Torres, but the Lake District is pretty (I would characterize it as enjoyable, but not spectacular).

I went to Iquitos in 2017 and spent three nights at a jungle lodge in the Amazon area. The Amazon itself is amazing, and I enjoyed seeing the river dolphins. Fishing for piranha is fun, etc., but I was not impressed overall with the wildlife I saw -- I saw more wildlife in less time in Panama.

You are correct not to focus a trip on Iguazu. Iguazu is amazing, but you can see everything in two days -- one on each side. It is, as you say, something that you combine with other stuff in either Brazil or Argentina.

Panama is great in that you have incredible rainforest in less than a 30-minute drive from your hotel in the capital. You can stay in the city and see the canal, enjoy the old part of the city, and then you can go to a park like Sobernia and see absolutely incredible nature. Sobernia has the world record for bird species seen in a day. And besides the birds, in my day of hiking in the park, I saw incredible blue morpho butterflies, two kinds of monkeys, coatis, amazing trees -- it's just amazing hiking.

Also in Central America, I think that you should consider Guatemala. Antigua is a great colonial city, but the mountains surrounding it are spectacular. Spend several days there, and then go to Lake Atitlan for a few days. Again, the scenery is great, but the very different villages around the lake (different Mayan tribes that speak different languages) are also really great.

I've never been to Colombia or Brazil (outside of Foz do Iguacu), I want to see Angel Falls in Venezuela some day, I want to hike in Ecuador, I've never been to Atacama/Uyuni, Lake Titicaca is great but also not the focus of a trip,

Ultimately, if you dive, then you should absolutely choose the Galapagos. If not, then it's a tough call, but I probably choose hiking in Patagonia.

Went to Amazon lodge through Manaus Brazil. Was very interesting but can’t say I’d go back unless it was for a sport trip like fishing. Would love to go to Panama or somewhere with more diverse scenery. The Amazon was beautiful but much the same every day. Like boating around the Atchafalaya for 5 days. Great but got monotonous.

Have been all over south America. Patagonia and the Amazon were both incredible. We did the Amazon through colombia (leticia). Awesome experience