Well, I mean, really it’s up to you if you want to go to San Sebastián or Barcelona as your one destination in Spain, although I’m confused: you said no one wants to go to Madrid, but you plan to go to Madrid after San Sebastián.

What it boils down to is this: San Sebastián is a smaller city, it’s located on Spain’s green/cool north coast, and it’s located in Basque country. Barcelona is on the hot/dry Mediterranean, it’s in Catalunya (in case you’re interested in that region’s culture), and it’s a big city. Which do you prefer?

San Sebastián is a lovely city, on a lovely bay, with a nice beach, and a charming old quarter. Barcelona is a big city, it’s a great city architecturally, has an amazing old, medieval quarter (the Barri Gòtic, which is medieval, but with extensive modifications in the 19th/20th centuries, which is why it’s still standing), as well as plenty of great 19th and early-20th century architecture in other parts of the city. And if you’re a big-city enthusiast like me, the city’s gentrification/transformation of its waterfront (as well as some inland quarters), are highly worth a look. Depending on how many days you plan to spend there, you can also take some daytrip(s) or overnight trip(s) to elsewhere within the Catalunya region, including coastal beach towns.

Both Barcelona and San Sebastián are connected to Madrid by train. Barcelona is connected to Madrid (country’s two largest and most important cities) by AVE high-speed rail. Here’s a great German website that actually lets you check train schedules throughout Europe.

Check that website for the San Sebastián-Paris run. I’ve personally done the northbound route, about ten years ago. It was a short train ride from San Sebastián to the FR-ES border (Spanish town called Irún), then we hopped on a French high-speed TGV train to Paris, and it was overnight. If you do end up finding yourself boarding a TGV train from Paris to Irún, keep in mind that the train only runs on designated high-speed tracks for less than half of the journey, then it runs on conventional tracks, because there is no high-speed track from Paris all the way to Irún. So, if you do find yourself on an overnight TGV (as did I), it will be a long, overnight trip…not a 3-hour commute.

And in case you’re wondering, all trains between France and Spain either terminate at the border and you’re forced to switch train, or the train stalls at the border, and they change the wheels on the train as the passengers wait inside the train. This is because the gauges are different: train tracks are wider on the Iberian peninsula (Spain and Portugal) than in the rest of Europe. The only exception is Spain’s AVE high speed tracks, which have the same gauge as the rest of Europe…but no high-speed tracks have been built to cross the FR-ES border yet.

What Luv said.
I really loved San Sebastián, and would return in a heartbeat.
We took the train from Toulouse to Pau to Hendaye at the border, then the EuskoTren to San Sebastián.