I like the new system and i don't miss percentages. The problem is rather that hard disables are so easily available and easy to apply. I think the idea that you have to apply multiple debuffs or debuff chains to get a disable is a better idea. We have this with wet and freeze i think ? This could be expanded further. So that you can't apply knockdown in a single round or single turn and that the other side has a chance to counter your incoming disable.
The point of mixed damage parties being worse is not a inherent problem to the current system. It is simply a problem of balancing. If you had enemies with say 6 or 8(<-- these number would need fine-tuning) times more armor of the other kind, you would be in a better position if half of your team could deal the lower damage type. If the majority of encounters had enemies like this, mixed parties would even be favorable in comparison to pure damage type parties.