We did the first option u mention and loved it. Its very easy to fly from santiago to Punta Arenas and make your way to TdP, which is fabulous. From TdP u can take a bus to el Calafate. Not sure how one does this, but I have read that u can do it. We drove back to Puerto Natales and took the bus from there, but we were away for 6 weeks so had lots of time. then fly to BA from el Calafate. We did the mini trekking on Puerto Moreno and it was very cool. Have u been to these places before?
Yes, it is very easy to arrange everything on your own.
Check out our TR http://www.fodors.com/community/south-america/southward-ho-adventures-in-chile-arg.cfm

Always Glaciers and others offer transfers directly from the park to/from El Calafate. It costs more than the bus but you save a lot of time.

If you are interested in seeing penguins, don't miss Isla Magdalena - it's absolutely magical and by far the best penguin site we visited in Argentina/Chile (much better than Otway and Punta Tombo). You may even be there late enough that the chicks will be hatching!

The buses between Punta Arenas, Puerto Natalas, and El Calafate are pretty straightforward. You have to get tickets ahead of time, and confirm your tickets as well. The border crossings take awhile, but are straightforward.

Sadly, I was in Torres del Paine during the forest fires in December/January, so I'm not sure what shorter hike options are available, but in Puerto Natales itself there is a beautiful hike (not too long) along Laguna Sofia.

There is also a great hike near Mt. Fitz Roy in El Chalten, as well as the possibility of a glacier trek on nearby Viedma glacier (although I hear hiking on Perito Moreno is better).

Thank you, guys! Your answers are really appreciated.

Yestravel, no this will first time for us for Argentina and CHilie. We have been to SA before, but not these countries. And you trip report is fabulous! I started reading last night, but will finish tonight. Too much to take in! Unfortunately, we do not have luxury of time. We will only have 2 weeks.

Huentetu, thanks for the tip on transportation. I actually worry about this the most.

Travel_monkey, thanks for a great advice about penguins, and everything else.
I think I will try to book an open jaw flight - CHicago - Santiago and BA to Chicagol

I think an open jaw as u described is good. U can always fill in the in-between--lots of choices as you r discovering. Glad u r enjoying the TR. It was a fabulous trip--just beautiful scenery and wonderful people. We ended in BA which is not in the TR, our third time there. Great city!

Yestravel, thank you again! I will book my tickets and come back with more questions...

I just booked international tickets, so now have soon come back with some questions on details.
One of them, I really would like to incorporate Iguassu Falls, but then I need to skip peninsula Valdes, so I have 2 extra days to go to BA and IGU.
Does it make sense?
And I just found out that visits to Magdalena islands start only on December, we are going in November... too bad..
So my general route so far Satiago -Punta Arenas - Torres del paine (not sure how many days here) - El Calafate (a couple of days),El Chalten (not sure) and then I am not sure - Puerto Madryn, or IGU. And we will end in BA.

If you click my name and scroll down to Feb 09 I have a trip report for Chilean Patagonia. You might be able to see penguins at Seno Otway but I don' t know if November is too early. As you can tell from my report I loved La Casa Escondida not far from Punta Arenas airport. Read the TA reviews! Torres del Paine can be viewed in a day or two if you are not hiking. And if you are going to Perito Moreno you may not want to go to Glacier Grey. I think November can be even more windy than usual so limiting the sea excursions is a good idea.

I went to Seno Otway in November and the penguins were there nesting. I don't think it is as large a group as at Magdalena, but it is a short drive from Punta Arenas (less than an hour I seem to recall). When we were there, most people went late in the afternoon, 4 or 5 p.m., as that is when they were most active (males and females change places taking care of the nests).

Agree with the comment above--Perito Moreno is the more impressive glacier and has the mini trekking, so if time is short, concentrate on Perito Moreno.

I haven't been to Peninsula Valdes, but I think Iguazu offers more variety. Was there also in November, and had very fine weather. Not the highest water level but was still pretty impressive. Two days is just right, but you could see the Argentine side with just one overnight if you need to for time.

We found the Peninsula Valdes to be rather disappointing. The animals are generally very far away, and we only saw a few elephant seals (note that the seals are seasonal). We had seen many guanacos and rheas, as well as penguins, in southern Patagonia, so Puerto Madryn felt unnecessary. The beach isn't particularly nice. Punta Tombo (~1.5 hours south of Puerto Madryn) does have many more penguins that Otway, but you will still see the penguins at Otway, just smaller numbers of them.

On the other hand, we were surprised how much we enjoyed Iguazu, even with the crowds. We spent two nights there, including one full day at the falls, and had a great time. The falls are beautiful (in January), and we saw capuchin monkeys and coati babies. I definitely recommend the boat tour that brings you up under the falls - it was worth it! With our extra half day (before returning to BA), we visited the animal sanctuary, which is great if you really like animals and want to support the sanctuary's work.

If you go to Iguazu, don't hesitate to stay in town, rather than in the park. It's less expensive, has more restaurant options, and the bus runs often.