Back to the mines, I would personally like to see an ability where you could manually detonate an entire array. So you could wait until the enemy fleet is well inside your field and then get the biggest benefit from the splash rather than having the mines destroy a few lead ships while leaving the rest of the fleet untouched.
The "Detonate" ability could become an active ability rather than a passive as it is now, and you could turn off the autocast for a selected swath of the array and then press the trigger when you feel like it. Sort of like the scuttle action except the command applies to all selected mines instead of just the subselected one.
Also, I'd like to see ion abilities or weapons or mines that disable the abilities/weapons/engines (maybe shields? They draw on a power supply, right?) of targeted ships like there are in many mods.
On top of that, I also think that after almost half a century, the races would have come up with more shield piercing weapons like the Vasari have. Shields are only the first line of defense for every warship in the sector so scientists for the TEC and Advent must have been trying to copy or steal phase missiles this whole time like they copied/stole phase disruptors.