Spain and Portugal

If you are using public transportation, from Madrid you can easily do day trips to El Escorial, Segovia, and Avila. There are great museums, Retiro Park, and other sites in Madrid, as well. In Lisbon, I'd suggest the Monastery of Jeronimos, and a day trip to Sintra to see the National Palaces of Sintra and Pena. If you are renting a car, there are a number of interesting cities between Lisbon and Madrid. To get the teens involved, you might want to get them to look at a basic guidebook or websites for these two cities and specific sites.

Just wanted to second what Anita posted re: daytrips and add:
Lisbon - definitely Sintra and Evora (if you're interested in Roman ruins)
Madrid - Toledo, Segovia, Avila, and Alcala de Henares (if you're into architecture)

Is it possible to do an overnight in Toledo? If so, I would!

Thanks for the great tips! We are definitely going to try to stay in Toledo over night. Love the rest of the suggestions too.

We are also trying to have the kids take a larger role in what we do, but they are pretty easy going and are simply excited they are going to Europe. As we make plans we will definitely be checking in with them to make sure they are on board too.

The old university town of Coimbra is another great stop in Portugal. You can catch the overnight train to Madrid from either Lisbon or Coimbra; there is no daytime train. There are daytime buses between Lisbon and Madrid by www.avanzabus.com (2x/day, 9 hours). For flights, try www.skyscanner.com.

We were in Madrid in November of last year for an entire week, and could've used more time there, between visiting museums, the Royal Palace, and day trips to places mentioned above. We rented an apartment thru HomeAway.com in the La Latina neighborhood, which allowed us acces to a washing machine and a full kitchen for breakfast.

We went to El Escorial on a Wednesday, when there's a farmer's market, and assembled a great picnic lunch before touring the famous, historic palace/monastery.

While you could spend all 13 days in Portugal (Evora also has a fascinating nearby Neolithic dolmen site, and Obidos and Porto, north of Lisbon are worthwhile, too), maybe 7-8 days in Spain and 5 in Portugal would be a good mix for this trip.

Maybe 3 days in Lisbon (with a day to Sintra) then fly to Seville for 3 days.
Then AVE high speed train to Cordoba for 1 day.
Finally on to a Madrid apartment and 6 days for the great art museums and aforementioned day trips.

For travel within Spain and Portugal, a good site I have found is goeuro.com. It
is easy to use and gives you info on air, bus, train and car travel times and costs between each place, all on the same page, so no flipping back and forth between sites. It also gives you the scheduled
times for bus and flights.

A HUGE thank you to everyone for you tips and suggestions. We are set for six nights in Lisbon with day trips across the region. We will fly to Madrid and stay for a few nights. We'll take an overnight in Toledo and Ronda and end in Sevillle. Should be a great trip!