We're going to chalk a lot of this up to PGI being really bad at explaining things. What I've learned about the Queues comes from Tweets w/ Russ, Karl Berg's thread and personal observations.
So, having said that....
First, what happens in the Ghost Queue.
This is the pre-matchmaker where groups are put together. It is FIFO, but it is
biased to making 12 as quick as possible. Say 60 people queue up on Wazan. The Ghost Queue starts putting groups together in a way that creates 12 the fastest. 10 man and 2 pugs, 7 man and 5 pugs, etc. If suddenly a 5 man enters the Ghost Queue and a 7 man is already waiting, it will purge the pugs from the 7 man group and put the 5 man in it's place (This is where you'll suddenly see a large group of Pilot Awaiting Orders" suddenly dump from your queue)
At this point, no group (unless it's a prebuilt 12 man Unit Group) is actually put together, it just has the combinations built and waiting for the next Zone Queue to open, during this time, if a player or group drops from the queue, it is rebuilt as best as can be, but may determine it's priority position based off of FIFO. (if that 7 man that was in the queue the longest dumps out, the 5 man that was placed with it suddenly gets put back into it's original place in line)
Once a Zone Queue opens up, it takes the group who's members have been in the Ghost Queue the longest and places them in it.
How Zone Queues work (Attacking a Planet):
When you queue up to attack a planet, and you have spent the time in the Ghost Queue getting your 12 players tetrised together it then puts you in a Zone Queue, this is where one of the 15 zones has been selected for your attack on, all the while it has been chewing the Defenders Ghost Queue to put together 12 to defend the zone.
This is why it takes anywhere between 1-10 minutes in the Zone Queue before you get a match. If a Defender for your attack is found, a 1 minute count down starts, if no defender is found by 10 minutes, a turret drop is launched. At any point during the 10 minutes a defender can be found then the 1 minute countdown begins (I've actually been in a couple queues when we got down below the 30 second mark, and it kicked back up to 1 minute because an OP4 was put together).
Once that match is created and launched, the Matchmaker goes to the next zone available and pulls a group of attackers out of the Ghost Queue and begins the process again.
While this may seem like a lot of wasted time in the queue, I understand it as a stop gap to slow a planets acquisition via turret drops. If it didn't run this way, then 5 groups could get together and take a planet from 0 to 100% in as little as 45 minutes if it is undefended.
I agree there should be a happy medium between this, maybe the zone queue firing off faster if there are active defenders, I'm sure this is a WiP we'll be seeing SoonTM
How Zone Queues work (Defending a Planet):
Take all the information I've given above, now apply that to
only if there is an occupied/contested zone. That is to say, there is nowhere for the Zone Queue to put you if there are no attackers OR there are no zones that have been taken by attackers. If the above are both true, then the Zone Queue pulls from the Defenders Ghost Queue once an attacking 12 man has been tetrised by the Match Maker.
Now, looking at the numbers by themselves, they don't tell the whole story of the queues. Just because the numbers are divisible by 12, doesn't necessarily mean that those can be put together to make full 12 player units. Just an example of this, you can make 24 with 3 8 man groups. While this is extremely edge case, there is absolutely no way for the Ghost Queue to fill a Zone Queue with those players.
This is why I've been pushing House Marik groups to break up into solos or small, even numbered groups if they can't make a full 12 as it maximizes their chances to get into a drop quickly.
Having said that, there is also a vital piece of information missing in your example above. in the 36/48, I'm assuming you mean 36 attackers and 48 defenders, and IIRC, you said you were defending on that planet. I have to ask this. how many zones were occupied by the attackers? Did the Zone queue have a place to put you where you could do a turret drop while the other attackers were engaged with other defenders?
In the situation you describe, providing the Ghost Queue was able to make 3 full Zone Queues with the players in the queue, your queue shouldn't have taken more than 13 minutes (1+ minute count down, best case, for each of the previous 3 Zone Queues to get in a match + 10 minutes for the other 12 players to get a turret drop on Counter Attack IF there was a zone available) before the next Zone Queue fired off a 10 minute count down for the next zone to be Counter Attacked IF there was a zone available.
I know that there are ways to improve Queue Times being worked on, and that better planetary information would go a long way to alleviating some of the frustration (also being worked on), but I hope all of this explains what's really happening and why.