I flew Madrid to Paris and return in 2012. The flight was ok, but I would not do it again. Vueling Airlines....had flown them before with good success. But on both trips they cancelled the early flight I had made a month or two before and then put me on a flight from Madrid to Paris 4 hours later....then that flight was delayed by 3 hours - no specific, honest reason given -- messed my schedule up completely...and the same on the return.
Check out the site The man in seat 61 for specifics on train travel. I will take the train from Madrid to Barcelona and then on to Paris should I make the trip again. The AVE train is an excellent mode of transportation. No long waits before departure, etc. Smooth ride...and you can see the countryside as well..