I have a whole list of reasons why I like how the individual queues are and why a master list might not work well at all... but when I tried writing it down in a few short thoughts it became this like mini essay... so instead of the mini essay I'm assuming no one actually wants to read I'll just put this little blurb of why I like individual Queues as a challenger and hopeful future gym leader.
Individual queues are efficient for both gym leaders and the challengers because challengers can be on multiple queues at once and gym leaders can choose how they personally want to treat the queue. Though occasionally a Gym leader will accidentally let their Queue list fill up too much so they have to cut it or stay longer then expected, it's not the biggest deal in the world, it's up to the gym leader what to do, quite a few seem to just cut the list and often let those they cut get pushed to the front of the line the next time they come around, which I think works nicely. Even when they don't do that, it's not like I've ever seen a gym leader cut a line without being apologetic about it. (though I might be digressing a little)
I won't touch upon how long gym leaders spend battling though, I agree compeltely with SandstormS and have nothing to add myself on that matter.