I love to fly WN in general, but I HATE connecting with them, especially in PHX. If you're late or you have a tight connection, or if your connection involves a concourse change (which mine almost always do, it seems), you arrive at the connection gate to find that your boarding card is #138 out of 139.
What WN needs to do is either allow you to get cards for your entire itinerary when checking in at your origination station or create a Web Check-in process (similar to Delta's, which I'm trying out this week) to allow you to get all of your cards.
The result is the same: those who give a crap about what seat they're in still have the advantage. If you really care about your seat, check in online before the flight.
Right now, lines are the biggest problem at the airport. With most carriers, you have two: one to check bags/get boarding documents, and one for security. With WN right now, you have at least three: one to check bags, one for security, and one to get boarding cards. Then, when connecting, you have another one.
It's a big turn-off for people like me who more often than not have to get some real work done on the plane. In a middle seat, I can't get to my carry-on if I need something from it, and I can't really open up my laptop comfortably to do work.
I gotta hand it to WN for their service: everyone is friendly and geared toward solving problems rather than spouting the company line, and I love to fly them, but I simply can't if it involves a connection. Here in SAT, that means that most places I need to go, I won't fly them, unfortunately...