We did a similar trip last Oct-Dec here is a link to our blog which may provide some ideas.

http://www.travelpod.com/travel-blog-entries/candcthai/1/1222291440/tpod.html#ENTRY_LIST

We did not stay too long in Santaigo so cant really comment but we loved Valparaiso and the surrounding area. Som ereally great restaurants and teh graffit walk is a must do. We also spent a great day out near Vina horseriding along the beach, woods and teh biggest sand dunes I have ever seen. Not sure how viable it is to cross the Andes at this point into Mendoza as we crossed much further south from Pucon to San Martin where the Andes are much lower.

Mendoza was nice and a great place for food and wine (which seems to be a focus of your trip) but it was not my favourite place in Argentina.

The weather in Nov was ok for the beach in Montevideo but it seems along way for beach time. Colonia was a nice quaint place with beaches just outside of the town and the locals were swimming but being a river estuary , dont expect crystal clear blue seas!

BA is fantastic but huge so pick your loaction carefully. Palermo and Recoletta are the usual suspects but they are large area in themselves. Tigre may be an alternative to beach time and is easily accessible for a day trip. The weather was mostly hot in BA when we were there in nDec but I am not sure that this is always the case

Thanks for the info, great blog! This will be very helpful in planning my trip. The Horseriding near Vina del Mar looks fantastic.

What was your favorite place in Argentina?

Also, I would really like to fit in a rural town, which might happen during the Andes drive, but not sure. Any suggestions for a great village experience?

I feel NW fits in what you are looking for perfectly and maybe offer you a really cultural mix for you to "squeeze" your short time.
Do not miss Purmamarca, Tilcara, Salt Flats, Humahuaca and Cafayate ( our wine country) and you will love the weather and the food in this area.
If you need more info, feel free to make as many questions as you consider necessary.
Flintstones

although the NW looks beautiful, I'm not sure I would like to put that focus on my first trip to South America. I am more interested in the cities with tiny bursts of nature pieced throughout my journey.

And I'd like to shorten travel times as much as possible, but I'll have to keep in mind for my next trip though. Can you reccomend anything similar that's along my planned route??

Weather in November is ok, it's almost summer here in BA and it starts to feel hot. However, it isn't beach season yet. Summer holidays start almost in mid December so you won't find too many people in the beaches. The same applies for Uruguay.
Spending some days in the Delta in Tigre like crellstone said would be a good option. In the islands there are many bungalows or lodges with specially prepared beaches and you can also do some outdoor activities.
In BA, you should take a city tour to see the main spots of the city. then in your free time you can go back to the places you liked most

My favourite place in Argentina was the north west around Salta - the scenery, people and food were all amazing and our intention is to return there permanently in the (hopefully) not too distant future. I do however, understand your reasons for leaving it out on this trip.

other favourites were puerto madryn on teh Valdes Peninsula (for the whales)and Iguazu falls but both are a long way to travel just for a day or two. The one place I really regret not visiting was the glaciers in El Calafate

I cant help you with a small rural town which is on your route. As you will see from our blog we staed in loads in the rest of Argentina. The only one we stayed at in Mendoza province was San Raphael where we were looking at property, but unfortunately it did not live up to the hype on the web so I would not recommend it. I am sur you will find somewhere when you cross the Andes.

Rachelanneb, I hope one day you could visit this area and I am confident you will fall in love with it. Like Crellston! Like many others... You miss it! ;0)
Have a great time in Argentina!
Flintstones