Just raged about it few days ago in the shoutbox...
I mean okey if you are playing as a new AT team (diffrent configuration) the game will give you a very low elo because you are a "noob" in the eyes of the game... so the first rounds will be against noobs (which is in mind completly unfair)
The game should remind players based on their whole stat although they are playing with another team.
New players will definitly leave the game if they are getting rekt all the time... not very beginner friendly Relic.
So rank 1-50 players still get 10000+ players which will let to frustration for both sides which is poison for the game.
But yeah also the playerbase is not large enough thats another problem
still I think some kind of a skill level based on every game mode or faction would be the best solution (see the idea of helpinghans with the elo faceplates/level)