I've spent a few months in SA and would advise that with only two weeks you really need to focus. It's huge, and you'll eat into that time before you know it!
Galapagos is incredible, and you can do it pretty cheaply by staying on land (instead of a cruise). Excursions are pricey, but you can't beat the snorkeling there (just check out the time of year you go as the water can be very cold some months!).
Patagonia (Ushuaia is at the bottom of the continent) is amazing, and somewhere I want to go back to, but that involves quite a bit of trekking on glaciers, in the Fitzroy mountains and Torres del Paine, so maybe not ideal at the mo.
Argentina and Brazil both great, but huge!, and yes I do think possibly a bit touristy in Brazil. If you go there, go to Fernando de Noronha, which is a tiny island off the north-east coast which is a protected reserve. It's absolutely amazing (or it was 20 years ago!!) and I think a worthy bucket list destination.
Chile I'm a bit 'meh' about. I think there are better places, and a huge part of the country is lakes which are very hard to travel down. I didn't see Atacama though, which I'm sure would be very cool.
In your shoes, based on what you've said, I think I'd pick Colombia. I haven't actually been but know a lot of people who have and they absolutely rave about it, plus it's a good size for two weeks without racing around.
Damn, this has really made me want to do back now, it's such a brilliant continent!!