Seville-Córdoba-Madrid in 6 days

You have given yourself only one day in Madrid--a city you have to transit because of the outbound flight--so I would definitely not add another location. Aside from its own attractions, Madrid has magnificent side-trips. You'll have to hold off on Toledo, Segovia and Cuenca for now.

You may still be able to save a fair amount of money on train tickets by buying now. Both of your trips will be on AVEs, which can be costly if you pay full fare. Go to renfe.com and compare the cost for today's tickets vs. tickets for your planned travel dates, then decide how much the flexibility is worth to you. Of course, buying the Seville-Cordoba ticket ahead of time is a bit risky since there could be a delay on your flight from Berlin. http://www.renfe.com/EN/viajeros/

Thanks. I appreciate the help. Just one more thing - could you please elaborate on the side-trips in Madrid that you mention?

You aren’t spending any time in Madrid?
Do not even consider any day trips until you spend some time in that magnificent city!
Once you have spent some time in Madrid, day trips could be Toledo, Segovia.

I guess, I would argue you don't need to spend any time in Madrid, especially if you will be back to Spain. Some people like smaller towns more than huge cities. In the countries I've been to, I've covered the larger cities in multiple trips. I do agree that you couldn't add more in your itinerary with six days. Do you have your tickets? I should think you could fly in or out of Seville. If you flew into Seville. You could then train to Cordoba and then finish in Madrid.

Toledo is one of my favorite places. It has a huge historic district with some lovely Moorish-style buildings and is worth staying at least two nights, though most tourists treat it as a day-trip from Madrid.

Segovia has the stunning aqueduct and some intersting architecture of its own. It can fill a full day.

Cuenca has an atmospheric historic district on a hill that's bordered by a ravine. Some of the houses hang over the edge. There are also two good modern-art museums. For those interested in art, it's worth staying overnight.

Consider those places for your next trip to central Spain.

While train tickets would be cheaper if purchased today, a number of Spanish routes and departure times are still not available to purchase for October travel. So, you haven't necessarily missed anything and may even have to wait.

I'd stay in Madrid and leave the day trips for another time. At least go to the Prado and I believe everyone should see Guernica once in their life. There's the food markets and the tourist office located in Plaza Mayor has daily guided English walks around historic center.

Thanks for all the suggestions. I was thinking of a slight change in itinerary - instead of staying overnight in Cordoba on Day 4, would it be better to do it as a day trip en route Madrid? i.e. on Day 4 we start from Seville to Cordoba, stow our luggage at the bus station, visit Cordoba during the day and take the evening train to Madrid. That way we'll have some more time in Madrid.

Day 1: Arrive in Seville (3N)
Day 2: Seville
Day 3: Seville
Day 4: Early train to Cordoba. Store luggage at bus station & visit the Mezquita. Late train on to Madrid (2N)
Day 5: Madrid museums, or day to Toledo / Segovia
Day 6: Madrid sights before evening departure to Berlin

All you need to know about spain => http://travelinz.com/spain-travel-guide/

Cordoba is my favorite Spanish city. Madrid is interesting and has 3 top-notch art museums. If you love European painting, definitely spend more time in Madrid. Sure there are also day trips from Madrid and Toledo is another favorite of mine, but you don't have unlimited time. My suggestion is to relax and enjoy. Less is more. Cordoba is lovely at night, much quieter than Sevilla and thus more charming and intimate in the well-preserved medieval area. Madrid is a big, bustling city. Choose whatever floats YOUR boat.

I really doubt this will be your only trip to Spain. It's so easy to fall in love with it.

Great advice, Chani!

Thanks for the suggestions. We decided to spend the night in Córdoba and take the next morning train to Madrid.

I like djp_syd's itinerary.

If you arrive in Seville earlier in the day (or at least before evening) and since this is your first visit to Spain, you might want to consider booking a Flamenco performance your first evening. See my post of 07.28.18, I received some great suggestions.
Jon