I would skip El Chalten unless you plan to hike. The mountain's often hidden in the clouds. It's also a long drive on loose (and in some places, deep) gravel road there if you drive.

El Calafate is good for the glaceir cruise and going to Perito Moreno. Check on the weather forecast before you buy cruise tickets though. Don't forget the pictograms between town and the airport (FTE). AR has flights that leave from EZE which may be good for your schedule.

As for Los Notros, only worth it if you plan to partake in all the included outdoor activities.

It'll be too early to see penguins at Punto Tomba in November. They start to nest between December and leave by mid March when the chicks are grown and ready to venture out on their own. Highly recommended though if you're there over the austral summer.

Could always go to Peninsula Valdes but try to be at Punto Norte durng high tide (orca attack).