I went to Paine and Patagonia for a week last March. Here are my recommendations.
1. Take the cruise, no on the (fancier) Skorpios line , but on the Navimag line. According to everyone that we met that did a cruise it's not onlu cheaper, but also supposedly much more fun.
Punta Arenas is probably worth a two day stay if you are intrested in visiting the Penquin rookeries, but definitely go to the Natural History, Anthropology museum in town (can't recall the name -- Agostini maybe)
If you love nature on the other hand spend the time in Puerto Natales and Paine itself. BTW - if you are even a little bit adventurous I would highly recommned that you rent a car in PA and go to the Park ( and Natales) in the car, rather than in a planned tour. The park is very big, it's not easy (or cheap) to get around in and I always felt trapped on the liitle buses. They did a decent job, but are 99% inflexible.
If you are interested I posted some of my photography at:
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