1. First, I would increase the X4 elements of the game. I like have each of the victory types are tied together in one way or other. But other then the military victory, the others seem to be some what weak.
Culture is too easy to stop, the Pirates, become non-useable at some point, and the super weapons are in there own little world.
Here what I would of done.
For culture, I would leave it as it is, but add a rebel units that attack the other faction for all factions. I would link this to culture, in which the time to each attack is reduced with each increase in amount of culture you produce. There for there will be more attack against other factions with less culture then you. It is much like the TEC Insurgency but you do not need to be tec, and your culture has more of an effect. Which adds an offensive part to the more defensive culture.
To counter the loss of Insurgency, I would add that under the TEC tree, that the TEC, can sell them some of there own ship, including capital ship. Each time the TEC sell one of there ships, the bounty on there head, is reduced, by 2 times the value of those ships sold. There for keeping the TEC econ. edge, even during late game, were the Pirate force, can be easy to stop.
For the super weapons I would remove the Kostura cannon and the RA, and in it place, put the Rebuild Armada, in which every fleet, gets a bounes just, for being a fleet. This would remove a lot of the problems, that RA, seems to all ways have. I would keep the Advent deliverance engine, as the way it is, but also add, that when it hits a planet, there is a rebel attack at the moment. The fleet of rebel ships, will not attak you for 5 mins, after that, they will attack you too. For the TEC, I would replaced the Novalith Cannon with a the super fighter upgrade.
2. I would make it so that the strike craft problem was fixede in advance, as well as to produce a real diffence between the strike craft of one faction, to that of the other, but make it easy to learn.
Here what I would of done.
Make it so that the closer that a strike craft group is to there carriers, the faster, that they rebuild. There for, you half to risk your carrier, in order to save your strile craft, or risk your strike craft, to save your carrier.
I would change the strike craft in these ways.
For the Vasari
I would of gave them "Phase mines", which attck like fighter, that ram into there targets and explode. The Phase mines can sit in wait like fighter, but can also jump to other systems, but do are destoryed, when they hit there target. On top of that they take twice as long to build, an there for do less damage over time, the long it takes, for them to reach there targets. They do as much damage, as the first run of any fighter group.
For the Advent
For the advent, I would keep them the way that they are, but make them harder to hit, but would add special abilities, like splash damage, and other passive abilities.
For the TEC
I would give them super strong fighters, much like the Vasari are now, but allow for them to reach the numbers of the advent, after there super fighter super weapon comes online.
For more details, just post and I will add more info.