The issues I see with the war system, in no particular order are:
* Currently the EE system discourages growth for all but the largest accounts and actually rewards players for lowering CS (converting to GH/sh). There are several ways to combat this from limiting ee participation to a minimum CS; creating war brakets based on CS; basing payout on total strength of account including CS, BFA and BFE instead of just on CS (and BFA??); tightening up hit ranges;
* A lack of participation. This is due a couple of reasons, 1 poor match making leading clans that lose consistently, for whatever reason, to give up; because 2, the penalties for losing are massive, 5 bil in pots, 0-7 bil in mith (much more if casting max mith), 4-9 bil in 2-3 hours of lost EB time, an xtal, an ee level and most painfully a rancor level.
I think removing the loss of a rancor level on war loss would probably be enough to increase participation as it would give the clans that win 30% or less of the time an incentive to continue as the will at least slowly gain rancor level and earn some of the uber equiptment instead of having nothing to show for a season of mostly loses...the number of rancor required to achieve each level would need to be increased if that were done.
* Static stats, especially BFE and BFA, but also towers being very undervalued in the matchmaking algorithm. This, coupled with the GH/sh stacking roster stacking to allow LB/GH clans to match a balanced roster mid heavy clan is the biggest factor in causing mismatches, as it's a no win situation because you can't win against lb and can't make any plunder off GH.
Increase the weighting of static stats as compared to dynamic, troop %, based stats and matchups would improve dramatically. Lb accounts would matchup against lb accounts. Increase the static stat weighting enough and it might even discourage the massive tower turtle builds which are becoming all the rage, almost required, for non LB/GH/sh.
Good luck fixing the mess you have wrought
