How to balance Phase Missiles
Thinking about the issue that late game (full PM research) any Vasari player can beat Advent with ease because their PM bypass the Advents primary defence (shields) I came up with two ideas to balance PM against Advent (which I believe is the biggest issue as TEC can always hold their ground with a group of Hoshikos).
The first idea is to change the repulsion ability (Iconus Guardian) so it deflects incoming Missiles for the duration of half its cool down.
Another similar idea would be to change repulsion to a passive AoE and give it only the ability to deflect x% of incoming missiles.
But the idea I personally like better would be to change the Vasari. You see, when they tried to nerf the PM the first time they took them away from the fighters and let them remain with the bombers. In my opinion it should be the other way 'round. Let the fighters have PM (but maybe nerf damage of fighters against anything apart from corvettes, LRF and bombers) and let bombers only have Pulse Wave Emitters.
My reasoning behind this is: When robbed of their ability to snipe enemies with PM bombers the Vasari have one big problem: Their caps are weak. That means that unless they have something to counter their enemies attempts to snipe their caps the Vasari will go down quickly. Especially since the Vasari's means to keep their ships alive longer are both cap ship abilities (Skirantras repair cloud and the nanite swarm from the Rankulas) and would thus require great cap ship micromanagement (to reach all frigates with the repair) and endanger the caps in doing so (by moving them closest to the front lines) or endanger the whole fleet (by packing all units closer together, which makes splash damage a bigger issue).
So I say: Give the Vasari a means to fend off any sniping attempt (by bombers, corvettes or LRF) by making their fighters stronger and at the same time take away their OP bomber weapons and replace them with something less powerful. (Maybe you could also reduce the range of the Kanrak to nerf their PM.)
That would also be a deterrent to huge bomber swarms since they won't do anything against an enemy Vasari with some fighter squads.