- Edited
Here are some ways you can balance mods:
1: First make your things way too weak, buffs are better than nerfs!
2: Make sure all of your systems have a counter, shields are countered by electro-bolts and EMP missiles.
3: Make sure that if your system has no counter, it is a counter to itself, make sure each pro has a con. For example: if you have an EMP weapon, try giving it a weak EMP effect around itself.
4: You can make weapons less effective at certain distances. Your opponent would just need to go far enough, Thanks @Alpha!
I'm working on more!