Currently missiles are way too good. They have several advantages over all of the other strategies. I will list them here, they:
1. Have the longest range.
2. Track their targets and accelerate extremely fast, meaning they guarantee almost 100% hit chance.
3. Are very hard to shoot down when fired in bursts.
4. Counter shields as they do huge AoE damage that forces weapons to be placed alongside the shields and not in front of them inside the barrier.
5. Can be auto-fired with range that spans the entire arena, meaning they have almost over 5x the range of other weapons.
If you combine this with the superior advantage that speed provides, you don't even need shields. Your ship will:
1. Kite faster than missiles can follow it.
2. Auto-fire to any ships following it with huge range.
3. And provided you place your reactors and armor intelligently, survive ion beam clingers and even split to independently operational pieces when broken. And those broken pieces still keep firing missiles with longer range than any other weapon from nearly any angle.
I give you Coffee's DEFF:
I have been enjoying the game a lot in its current state. I have developed designs that infuriate some of the players, pulling comments that claim I'm playing the game wrong. Suicide bombers, ion kiters with optimal shielding, clingers that counter Cerberus with fraction of the cost, kiter counters that double as sumo ships with the ability to push enemies out of the ring of death and then of course the missile kiter. An armada with roles meant to counter each other.
I have not been able to counter DEFF without coming out bloodied and shattered by the amount of micro-management it required. And those designs counter DEFF and DEFF alone, whilst DEFF counters EVERYTHING.
EDIT On top of this there is another issue related to reactor explosions:
https://forum.cosmoteer.net/d/5490-reactor-explosion-behavior-in-different-speeds
Even this thing couldn't withstand DEFF for more than 15 seconds.
I suggest either making the upcoming gatling guns able to shoot down missiles or implementing a flag cannon able to take down missiles in a huge area with a longer cooldown. The railguns could also be an option, but I doubt giving them a range longer than auto-fired missiles would be a solution. I hope this is addressed as I don't find fighting variants of DEFF with other DEFFs that much fun.