I would recommend at least a full day in Rio to see the sights, esp. if you plan to go up to the top of either Corcovado or Sugar Loaf. There is a LOT of heavy traffic in Rio, esp. on weekdays, so getting stuck in traffic needs to be planned on on any of the major streets or roads.
We just returned from the Ryndam (HAL) Valparaiso to Rio cruise, and use this company: www.southstartours.com
for our land arrangements. Always had a small group (3-10 people) in a van instead of a bus. Buses are not allowed up to the Christ the Redemer statue in Rio. Bus tours require you to take the cog-wheeled rail to the top, with much more lines, and you miss the beautiful drive up (and completely miss the drive down the south side of the mountain through the Tujica National Park) which can only be done by van or car.
We arranged our own tours (all but one through South Star) at every port, and not only had better tours, but much cheaper.
Our roughest seas/weather was south of Valparaiso. It was very smooth from Cape Horn to Falklands and on to Rio, which I had thought would be the roughest, but I guess you never know. It was COLD in both Ushuaia (wind) and Puenta Arenas. Take gloves, hats and heavy coats for this. Even in spring (December) it was in the high 80s in Rio, and can be over 100 F with humidity of 60-80% in their summer. Buenos Aires and Santiago very similar weather to Southern California.
Puerto Montt was my favorite port. We had a wonderful driving tour through the lakes, volcanos and waterfalls here. We used Eureka Turiso (a local company) there. I can get their email address for anyone who wants it. Whatever you do, get out of the town here and out into the country. Puerto Varas was nice, but very crowded as every bus from the ship went here (the German museum, esp.). Several people took the river rafting trip here and had a nice time (although some had to swim!).