Yesterday I've been unable to do some proper testing because it crashed after 5 minutes, every single time. Probably the memory limit, although I don't think my computer was over the 2GB level. I have large adresses aware on, so that would be the stability issue described in the tech support pages
If necessary try lowering you graphics (ship/structure/planet) detail as well, even if you're sure you have LAA. A few people reported having stability issues with LAA and that reducing graphics settings still helped. Perhaps for whatever reason LAA does not work properly on all PCs; sadly I have little way of knowing.
The first is that I doubt the power of the abilities of all capital ships. I use them as well as I can, I've used them in all sorts of combinations and I feel that there is no bonus whatsoever. My fighters aren't any more powerful, die faster than the imperial fighters, even though they're the ones outnumberd by mine and the enemy ships die slower than my ships, even though I'm very sure I've got more firepower than they have.
Alliance MC80 capitalships do different things, but all have abilities that either improve defense or provide healing. Combine this with further healing benefits from the Nebulon-B Frigate and Bulk Cruiser, as well as their durable late tier units like the Assault Frigate and MC40a, and Rebel fleets can be very difficult to kill. Just like the Battle of Endor, the main Rebel Fleet is intended to outlast its opponents while its fighters do major damage.
Per fleet supply your fighters are definitely a bit more powerful. They become easily the best fighters in the game when you get the Starfighter Doctrine research, since this gives an extra fighter to all squads, I.e. a +25-33% increase in the total HP and damage of each squad. The Imperials have more units that can deploy small groups of basic TIE Fighters but their units are also much more expensive.
Secondly, what imperial ship's presence forces my ships to a phase jump charge rate of 700%? I couldn't work out what else causes it.
Any of the Interdictor Cruiser units. I had to program Interdictor cruisers to work differently for the AI since they could not handle the complexity of using them properly. So they act as moving phase jump inhibitors for the AI. For human players they stop all hyperspace jumps, but only while they have antimatter, and they can be interrupted or will be forced to stop if they take enough damage.
The third thing is one ability that the empire must have, that completely ruined my tactic. I've upgraded my starbase with the no surrender ability, so that at least the enemy frigates would all die and I could then deal with the two stardestroyers. But the ability was disabled. Seems very unfair to me that the empire can simply get rid of a starbase (which is already considerably weaker than their own) without worrying about the suicide button. At least when fighting the TEC as Vasari, I had to keep my distance and do it with fighters and bombers (which completely didn't work this time with the Rebel Alliance)
There is not a whole lot of units that can disable Starbase abilities. However very powerful units, like the hero unit Grand Admiral Thrawn or Darth Vader (a titan) do have abilities that can accomplish this, as can your own Liberty Mon Calamari cruisers.
None of these units can keep up abilities disabled by themselves though, so unless there were several different units capable of doing it, you should have had some window to use the ability. It just unfortunately wasn't when you needed to use it.
This also brings me to the third part. Why do the carriers have weapons? They immediately went to attack a planet while I wanted to keep my distance and deal with the starbase first. While it's possible to do so, a single moment of dealing with a battle three planets away got them all killed because they went at it. While the dual role seems nice, it actually only adds tedious micro-management, which you already have enough of if you want the fighters and bombers to do a decent job. If they're really supposed to keep the bombing systems, it would be great to have it an ability with autocast disabled by default. Still micromanagement, but missing it due to whatever reason there is, will make it far less of a tactical liability.
Rebel QuasarFire carriers do not have weapons. However, they do bomb planets with their Y-wing squadrons. All Rebel units bombard the planet with Y-wings because they are typically against the massive turbolaser orbital bombardment so often used by the Empire. The Alliance is also all about dual role units, like their light Frigate, the CR90 being a minelayer and the Galofree transport acting as a special constructor for deep space stations and planetary Ion Cannons. If you are attacking a heavily fortified system I set all my units to local engagement range, that should help keep them out of trouble.
Finally, the carriers have a cost of 21 and can only come up with 2 squardons? Is this because of the starfighter doctrine later on or because of the multiple roles they have?
All standard carrier cruisers in this mod cost 21 fleet supply. This was a change from Enhanced 4X that tried to reduce the number of fighters (and thus lag) by increasing carrier costs and fighter stats by 50% over Vanilla Sins. Capitalships also had the number of fighters they can carry reduce to account for the stronger fighters.
I'm not really sure if I already had the starfighter doctrine available (have to look again next time), but if I have, will I see it in the form of being able to deploy 4 starfighters from a carrier instead of 2, or will it still be 2 with a copy for each of them automatically.
Sadly the infocard for Starfighter Doctrine is a bit misleading. It actually increases the number of fighters in each squad by 1. For some reason the infocard is treating it as a percent, as 1 = 100%, probably because this modifier was never actually used in the Vanilla game.
This is still very good for the Rebels though, since they have the smallest squads in the game. So X-Wing, B-wings and Y-wings get a 33% boost from this tech since they go from 3 to 4 fighters, while A-wings go from 4 to 5 for a 25% increase.