In next patch the penalty is reduced a little, plus throwers get a slight bonus on wpf.
Also, every time Magikarp whines about throwing the penalty is reduced by a further 1%.
Well this is good news, but it wasn't the WPF that is crippling throwers so much. The amount of ammo throwers have access to is what is really damning. 2 throwing axes, 1.5 jarrids/throwing spears, half a throwing lance per slot? Thats the biggest issue. If you change WPF per PT to 12, make Throwing axes, Jarrids, and throwing spears give 3 per slot, and have throwing lance go up to 1 per slot then things will be about right.
Also, slightly reduce the amount of ammo for the low-tier throwing weapons. 7 war darts? 5 or 6 would be fair. Right now low-tier throwing weapons are waaaaaay better than high tier ones.
P.S. I lawled in real life about the Magikarp comment