Dunno, in this version any fighter that is supposed to be around target for any meaningful amount of time is unviable later in the game. Missile spam could help via clogging PD weapons and possibly segregating targets so less PD and weapon overlap, but there aren't many options with medium missile slots for pilums in vanilla roster, especially carriers.
I assume this is due to more officers with anti-fighter skills plus the removal of damage reduction from player skills so fighters end up very squishy and the increase in replacement rate buff from the new fleet wide skill simply can't keep up in any hard fight. Which eliminates the previous issue of fighter spam generating way more HP to shoot at then most AI fleets could deal with but it kinda overshoots a bit where most of fighter wings simply can't provide much utility in bigger confrontations.
IMO if this is the case then there should be some sort of middle ground where either give something to counteract the anti-fighter skill or plain remove it. Alternatively it could be somewhat viable to remove fighter targeting from non-PD weapons but this also would make attack fighters extremely dangerous to destroyers and to a smaller extent to frigates (they would be zoned out of the engagement range of the carrier at best or get insta-swarmed and killed at worst). Also most projectile based PD is very inaccurate against fighters often failing to hit them even with decent tracking, but I'm not sure what the implication of improving their accuracy may have on missile effectiveness since such weapons also have the same issue where they miss a lot of shots effectively reducing their DPS to a fraction of what is listed.
Also on a less elegant solution there could be a different approach to fighter replacement where instead of being a constant linear production of fighters there could be a bit more variance. For example a fighter could suffer a great reduction of speed or straight up stick to the carrier for X amount of time after replacement but instead the carrier could rearm them faster or straight up every fighter in wing simultaneously hence their replacement rate won't dip so precariously after consistent loss of fighters. Although I guess there could be an issue where a carrier could end up in a situation where it can indefinitely kite a target as long as it has superior speed and sufficient fighters which is tremendously tedious to deal with and play as so maybe there could be some trade offs to be made. Although carrier as it is already loose their 0-flux speed boost while sending out their fighter wings but then again it takes the target some time to get their flux to 0 after fending off fighters too. Maybe there should be a significantly better replacement rate but the carrier will generate flux so flux will be the bottleneck for replacement rate instead of the current percentage while also removing 0-flux boost so you can't effectively kite with fighters? It would be a funny interaction with safety overrides, but at least it would also make more intuitive sense for a carrier since it currently mainly provides the constant 0-flux boost while not reducing carriers range in a meaningful way.
Although I'm not entirely sure why replacement rate is a thing and what purpose it serves so I may be brainstorming against that intention with such proposals so idk.
So far my personal play in vanilla I find carriers decent up to midgame, where you are dealing with ~200k independent \ pirate bounties or comparable fleets. Most wings are a decent addition as an increase of force per space, although I find warthogs being extremely handicapped by their abysmal engagement range. I know that their speed is bad, but 2000 ER makes them almost exclusive to legion, mora and converted hangar use. Interceptors are somewhat weak, but I speculate that they can be of use on cautious or steady officer as a fleet wide PD supplement. Haven't really tried this setup out though. Bombers are a bit of a mixed bag, tbh. It might be a good idea to maybe add more missile variants that go through friendly ships since it hampers some bombers in clutch fights like khopesh and maybe perdition \ flash. Piranhas have a weird interaction with speed boosts where it gets to the target way faster then it's able to shoot its bombs so they tend to circle around the target until they are empty. Or dead. So they probably should get some sort of workaround there, maybe multiple bombs per shot in a spread pattern with slower movement acceleration of the bomber?
Other then those, it's fairly OK roster to play with at that threat level. Although on higher threat it becomes way too dangerous to use any fighter with weapon range of 500 and less since there is too many weapons and missiles on the field creating no-fighter zones, and given how it can be fairly cheap on flux due to officer skill it creates a tangible disadvantage if you use such fighter wings as anything but a temproray HP screen \ escort. And at that point xyphos becomes one of the few options that can do something beside creating a quasi-threat for AI, but ironically they are best as converted hangar wing rather then being on a carrier due to the 0 escort range.
Bombers also quickly become inneficient since any bombing run will most likely guarantee complete loss of all fighters be it escorts or bombers so I instead resort to gaming the replacement rate where I use heron with mining pods and two cobras or, if I feel adventurous, two trident wings so total amount of bombers is within 50% of all fighters and minimizing the replacement time per bombing run in case where all of them die.
So far my cookie cutter late game carrier is heron with safety overrides, mining pods, 2 cobras and heavy blaster. Doesn't suffer from constant lack of 0-flux boost due to escort \ engagement spam so it can consistently stay in range of the target and the replacement rate hardly runs out unless someone manages to catch up with the carrier. Also can fend off any small ships such as frigates, which are probably the only non-SO ships that can catch up with SO heron.
Mora looks kind of nice since it has slots for pilums but no mobility system with base speed of 45 makes it a joke since it breaks off the rest of the fleet almost instantly and if the carrier can't catch up with the front line neither can fighters and especially bombers. But then again, haven't really tried to SO them so that might work. Although since you can't built in SO I'm not sure how much OP mora has and it can't have 360 shields like heron.