9 days in Spain with teen boys in July

I think Valencia sounds amazing, but with this time frame I would hold off and add more time to your existing stops, especially considering the feedback you got on the last trip. OR add some time in Costa Brava--sounds like your family likes outdoorsy things.
I'd actually save Madrid too--maybe head up into the mountains? A triangular trip from BCN is what I would find ideal.
But if you had your heart set on Madrid, there is absolutely nothing wrong with just Barcelona and Madrid.

Based on recent posts about pickpockets, make sure the kids are prepared (be mindful of phone, etc.)

Yes, flying in and out of Barcelona determines what is and is not doable on this trip. I think that I personally would reconsider these 3 bases. I understand how Madrid to Valencia circles you back to Barcelona but as much as I like Valencia I would skip it on this trip and substitue in Granada. You are right about the heat. It will be hot, particularly in Sevilla and Andalucía. Make sure you stay hydrated. So, although it is hard to narrow down your choices, just tell yourself and your family that you are just whetting your appetite for future visits to Spain! I think you are right in omitting Sevilla on this trip.

I suggest that in addition to your above planned route you consider basing in Barcelona, Madrid and Granada, or just Barcelona and Madrid.

Any way to dedicate those 2 Valencia days to Granada? I know you considered it and I think that would be a big draw for teens. The Alhambra is spectacular and I think you and your boys would love it. A daytrip to Toledo from Madrid is well worth it and if you were to have another day in Madrid you could daytrip to Segovia and see the castle and the aqueduct. Those would probably be very interesting sites for your sons. Barcelona has a lot to see and do so with those first three nights equalling two full days there you may not get to the Costa Brava if you keep three bases in your itinerary.

It will be a great trip no matter which itinerary you choose. There are no bad choices.

We traveled with teens quite a lot visiting Europe. We treated them like adults and did our touring visiting key historical sites, art museums and scenic places.

I love Barcelona, but suggest that you brief your kids to take special care of their valuable like wallets, passports, etc. Barcelona is the WORST city in Europe for pickpockets. Also, other criminal scams are a problem. Recommend wearing money belts.

Also, bike tours can be fun, my wife and I once biked quite a lot, and have done bike tours in Italy and France. The only concern we had in Italy for one bike tour was that while in a city, heavy traffic can give cause for safety, the way people drive in that country. Most of our bike tours used bike paths, which was fine, but when on streets, be careful.

Thank you for your suggestions! Perhaps we just do Barcelona and Madrid. We could add Costa Brava onto Barcelona and add day trips as suggested to Toledo and Segovia from Madrid.

Perhaps:
Days 1-2 Barcelona (2 nights Barcelona)
Days 3-6 Madrid (4 nights Madrid with Toledo and Segovia)
Days 7-9 (3 nights Barcelona and Costa Brava)

Thoughts on how to organize those days other than what I've suggested? I'm assuming Costa Brava is a day trip so no need for another hotel?

Thanks again!

The train is only 3 hours, so you could conceivably head to Madrid the day you arrive (good napping time), then return to Barcelona so you don't have to split your stay there. Of course it depends on arrival time and wherewithal for onward travel that day, but it can be a time saver in the end.

The only suggestion I guess I would add, is that each way between Madrid and Barcelona, you go through Zaragoza. It is a nice, maybe a bit overlooked town. Well worth two nights, a bit more laid back than the other two stops, and you suffer no real travel time hassle, since you pass right through. May be worth doing some looking at the town, if it interests, then consider.

Thank you to all who chimed in. It's hard as I'm really conscious of ensuring our teen boys in this trip planning. I am contemplating this itinerary for our 9 nights: 3 nights Madrid; 4 nights Barcelona; 2 nights Costa Brava

Day 1: Fly into Barcelona; Take first fight to Madrid as they appear to fly regularly; Rest from travel; Dinner and walk about in evening
Day 2: Madrid: Segway tour or hop-on-off tour; Bull fight
Day 3: Toledo; dinner in madrid
Day 4: train to Barcelona; afternoon acticivity
Day 5: La Sagrada Familia; afternoon activity; dinner El Born
Day 6: Montjuiic or Montserrat day trip (which one do you recommend??)
Day 7: daytime ?; paella cooking course in evening
Day 8: Costa Brava - boat cruise/snorkel/cliff jump and explore village
Day 9: Costa Brava - beach town and explore village
Day 10: fly home

Does this itinerary make sense and sound great? I'm open to suggestions. Also if anyone has suggestions of activities to fill in the gaps! Still deciding between Montjuiic and Montserrat. Also need to decide what town in Costa Brava to stay in. Thank you!!

On our Barcelona trip we spent a day on Montjuic Hill and very much enjoyed the breather from the city center. Granted this was 2011, but there were very few people up there and lots of walking paths and great views of the city. We took the cable car up to the top. We walked into the Olympic Stadium and had it all to ourselves. We walked around outside the infamous castle, visited the Joan Miro Foundation, walked through Botanical Gardens, and the fountain area. Of course doing Montserrat would be much more of an out-of-the-city trip and experience and I have heard really stunning. We opted to go to the beach town of Sitges instead. Personally I would cut the bullfight from your schedule, but that's just me.