I was going to say BCN, as the metro goes from both terminals to the train station and it is a bit shorter ride. As someone who flies SkyTeam, it is kind of a pain to get to Atocha, as you have to make your way to T4 via the bus.
I did Iryo from Barcelona to Madrid. Nice trains and the first class upgrade was cheap. Food and wine included. I had the same luggage you had and it fit nicely.