The balance mod idea might work pretty well. There should be some disadvantage when using weapons that fire every turn. Emissive armor would be pretty good answer early in the game, if it would work like it should. Later it wouldn't help because of the large mounts.
Another solution could be to make some weapons cheap to research but not very effective and others very effective but also very expensive to research. That way every weapon in the game would be useful at least for a while.
I hope we aren't going to balance the game to the point where only differences between weapons are name and picture.
