Hi, Trundle,
I'm happy to give you my opinion. I'm from the US, which means an early morning arrival in Madrid from an overnight flight. I do not plan to walk on the following day, so my schedule for the first couple days looks like this. Day 1 -- travel Madrid to Pamplona; Day 2 -- bus from Pamplona to Roncesvalles; Day 3 -- start to walk. I mention that because if I were hustling to get up to Roncesvalles on Day 1, my travel plans would be different.
For me, the easiest thing is to take a city bus from the Barajas airport to the Avda. de Americas bus stop. The bus stops right outside the airport terminal and drops you off at the bus station, making only a couple of stops along the way. If you read this thread, you'll see that I confused things a lot for Arlene by mentioning buses leaving more frequently than she thought they left. Turns out that the bus schedule depends on the day of the week, so you should check it at
http://www.movelia.es for your own arrival day. (seems like most days there is both a 3:00 and a 5:00 bus, though)
Here are the main points of comparison:
Buses take 5 hours, the train takes three hours
Buses cost 26 euro, the train costs around 50
Getting to the bus station from the airport is easy and cheap on the city bus #204. Getting to the train station is longer and more complicated (several transfers on metro) or more expensive if you take a cab. (If you're inclined to take a cab, the cab fare to the Avda. Americas bus stop would be cheaper than to Atocha train station but I don't know by how much).
Pamplona's bus station is in the central city (but I think there's a new one and I don't know exactly where it is -- surely someone can help us out here); and I think the train station is further out of town.
The first time I walked the Camino, I flew from Madrid to Pamplona, but it didn't really have much of an advantage because as you say, it's pretty much a do-nothing day anyway. So on subsequent trips I have used the bus and it's always worked out just fine. The bus station is in a busy commercial part of town so if you have a few hours to kill there are plenty of nice cafes nearby. I have never taken the train from Madrid to Pamplona, so I can't comment on it, but I have taken the train from Santiago to Madrid and found it a nice way to do the "re-entry."
Buen camino to you, Laurie