I made a post about mods the other day, I was thinking more weapon mods than regular mods. No speed secondaries, just upgrades to weapons that when fully upgraded gave an additional bonus that was Omega or Zeta worthy. I like the assist chance, cool idea. They could also have negative impacts for your opposition, like: -20% defense on hit when fully upgraded.
First mod, +5% offense. Second mod, +10% health steal. Third mod, +25% chance to stun. Full upgrade of any 3 mods: all allies gain 35% assist chance.
You could have so many different single mod choices to further customize your crews. Mods are the only difference between two mirror teams.