FCFS is not a bad thing. Until you realize that if you're trying to get to Hawaii from PHX and there are employees coming to PHX from PIT or PHL to connect to the same Hawaii flight, and if they're on HP metal they get to check in 12 hours before their 1st flight and they are automatically checked in for their connecting flight at THAT time, too. They would have a 6-8 hour (maybe more) advantage in check-in time. And once both HP and US can be booked in one res -- well then any connecting flight to those hubs, as well as CLT, that really early check-in time would count. With the time difference, especially, it's a huge advantage. Of course, when going from west to east those making connections from the west would have an advantage when trying to get to prime destinations such as Europe and the Carribbean -- but because of the time-difference, but it's not as big of an advantage.
So, having experienced both, and as much as I like FCFS, I think I would prefer seniority -- with a couple of "courtesy" rules, such as having to list at least 24 hours in advance (or go to the bottom of the list within your boarding priority) and checking in at least 1 hour in advance (or go to the bottom of the list within your boarding priority). And I don't have a lot of seniority, at all. It's just that sometimes it's not possible to be sitting in front of a computer at 12 hours exactly before a flight and if you're using a computer at a hotel and they're not using internet explorer, well then, you're SOL. With seniority, you know exactly where you stand and if the above 2 courteousies are employed, you can rest easy as no one "more senior" can bump you at the last minute or while you are in the air on your way to a connecting flight. Without these civilized restraints, then no-way would I want seniority to rule as that leaves too much wide-open for people to take advantage of those with less seniority.
Also, if my seniority doens't count for anything (if I'm not covered by any CBA) why in the world would I want to stay at this airline -- especially, as NewLowFare points out, there are a billion other jobs out there and they probably pay MORE?
But, knowing this airline, whatever is cheapest to administer is the way it will go. B)