I will still hope there will be a "disable all phase ships" setting at some point that also makes sense in the lore context and replaces these parts (so story doesn't mention phase nor there are any story phase fleets like the one when looking for Alpha Site). It's unfun and unfair to fight them, I fear a 4 DP shade or worse, pack of them more than a single Onslaught, against phase have to have 360 degree shields to feel safe and then there's the Harbinger who disables them and all guns, need heavy guns and flak pointing in all directions and can't chase them bcs of their disgusting speed (a Shade can still cross the whole map in mere 3 seconds despite the speed debuffs). Having to just sit there and wait for their CR to run out while curling into a defensive PD pointing everywhere ball is so much fun, or the fact they have literal invulnerability so you can't punish overextending unless AI is being dumb and I would rather not have AI be dumb, I want it to be smart and just not have access to phase. Phase and generally end game simply break how the game plays in an unfun way favoring high-tech, anti-shield, long range and constant damage at all times to either keep phase at bay or hit these stupid doritos who just zoom away if they want to. Once 1.0 hits it probably gonna be unfun teleporting, phasing and speeding time dorito battle station that also disables your everything and surrounds you with 20 mines while you can't touch it unless your entire fleet points at it with tachyons from all sides, even loot from them is unfun for low-tech enthusiast, it's all energy pew pews that mostly fit only in energy slots and are usually close range so only fit for fast high-tech ships and phase. I beat all of that on first try without S-modding everything with any kind of fleet but it is clear I do vastly better with high-tech ships and when being a cannons barrage enthusiast playing only low-tech ships fleets and listening to the ASMR, it makes sense low-tech is "low" but it's also sad Ziggurat will always be the best option, story expects you to have it and future end-game is going to be a chore unless played a certain way. Hopefully at least the lore will be fun (and a last ditch to get a low-tech tanky broadside ship).
Beams, SO ships with chainguns, fast frigates (tempest), devastators and HAG large ballistics all counter phase ships really well. Long range weapons to make them stay in phase longer so they build up more flux and slow down are also good.
I do agree that the main end game opponents being high tech is quite annoying. Either give factions mega fleets or swap some remnant systems with buffed derelicts so there are end game low tech fights. I suggested a sentinal style fleet made of Invictus and such ships because that would be scary as hell.
Omega composite weapons would be cool as well.