I've worked in games for over 25+ years. One flawed concept I see repeatedly in games is "This feature works great when we are successful". Most the companies that say that are out of business. Your match making system is based on that concept. When we have a ton of players it will work great, but what about when you don't have the players?
This game may need time to build an audience. It may not have 50,000 players online immediately. The Queue needs to not deter people from playing the game. In the company of 300+ people I work at, we play a lot of games. I am the only person interested in Dreadnought. I could not get anyone else to play because the Queue times are so long.
If you firmly believe your queue system will be better with more people, then you should open up Beta for a weekend and see if you get the number of players necessary to make it work. Else I'd figure a different structure for you matchmaking.
There are ways this game could have been structured to make a single queue work, to insure fast matchups, without a split tier population. Queue times need to be under 1 minute to be competitive with other games. If not, then you need an activity to entertain people while they wait, like a test area with A.I.s to fly around in your ship while you wait.