I think most of the problems are caused by low activity.
PW should only be run after steam (or on weekends) and with more factions to balance the meta game.
Regarding stomp - it is to be expected a bit, It is the hardcore version. We had the casual one too, where games would be balanced but it was deemed inferior to the hardcore version, also because issues like elo dumping.
Best we can do is to increase team size and add players.