Ok... I know your pain.

The ultimate question in MOBA, how to keep the MM fair and have a low enough MM time to be viable? How to have fun game modes YET maintain a respectable amount of players for each mode?

I know why you don't separate Skirmish and Elimination, it's probably during testing you found that they were unpopular and needed to be combined. I have a solution that will not only solve this problem, BUT make everything better!

When you queue for a game, simply provide the players a list of checkboxes. He/she can check all the games he's "willing to play". This way, internally you will queue him as if he individually signed up for each queue (you might have to work on some internal math for race conditions in case he get accepted on multiple games. Maybe have a single thread of games that gets filled before others, I don't know)

This way, the PLAYER decides which mode to play (and won't have to quit when he get into Skirmish instead of Elimination or whatever) AND he decides how much waiting he's willing to endure. You can even make it a "ranked" list, so the player can "prefer" duels, but won't mind if an elimination match came up first.

Thank me later!