Still got a few sprite problems with SS_windows and SS_windows4 right in the custom sprites folder, HorseMonster_DetailedWeapons\HM_wepEnergyTurret06a.png, HorseMonster_Realistic\HM_X_Sensors.png and HorseMonster_DetailedWeapons\HM_wepOneTubeLauncher01.png, DST BLU/Dst-ori87L, JWA_modified\spr_jwa_Kae_sml-sw06a.png and sw05a.png and a variety of shiny that came after the repack (that's not a big problem though).
Anyway, on to the missions:
1) A couple general things first. You should stagger your spawns to cut down on freezing, put a delay of 5 or so between each ship in a group and the game won't stick as badly . Second, the fighters (and probably other ships) can prove impossible to destroy under the right circumstances, i.e. when they're left with just their core and there are no allied fighters or ships with spammy enough weapons left alive. You could try putting a critical module on the section above it to make sure they're never left with just their core.
Aside from that the mission is pretty fun, the entrance of the larger enemies is great then the colossus showing up to tear through everything with ease is awesome. I love its machineguns cutting through the dreadnaught and other ships like butter.
2) You should probably make the portal bit of the gate rotate or something so it looks less static, it's kind of offputing in game. Aegising the gate makes it a bit unfair since it's essentially invincible and a perfect place to camp. Also, you might want to make it clearer that the science station can repair ships, I didn't notice that til halfway through this mission. All in all the mission is good but a lot like the last just the super carrier is less impressive, partly because it lacks machine gun swarms and doesn't make up for it with demeter swarms but mainly because it keeps running away - you should lower its ai range so it stays and fights. Still fun though, don't get me wrong.
3) The beginning of it was epic, big fleets, awesome beam cannons, a lot of fun to look at. Then the player gets his ships and they're honestly kind of useless, you feel pretty impotent because you basically have to wait til the super carrier does everything - I didn't even manage to take out two beam cannons (I guess splitting my fleet was a bad idea). Then wave 2 of enemies show up but it's pretty likely you don't have a fleet left so you just wait til the super carrier takes care of everything. Unfortunately this can take quite a while because the super carrier can be declawed pretty easily and its ai keeps backing away. All in all while the start was great I felt a bit useless in this one.
So, in general they were all still a lot of fun, concerns aside. That said, the whole saved by the allied super ship (or in the case of the last mission, spearheaded by it) thing is great but it gets old if it's done too much. Either let the player control the super ship for once or do something else. I'd also suggest giving the player a bit more importance at some point because right now you're essentially unnecessary backup and you know you'd win whether or not you were there (mission 1 is a bit of an exception).
Also, you've got a parenting problem in the T'sari dreadnaught, the rear wings are parented to the core so when the circle above it is destroyed you're left with floating sections. I'd suggest investing in critical modules or at least changing the parenting there.
Anyway, all my criticism aside these were a lot of fun, I look forward to more of them; so much so that I'll even keep BSF installed
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. However, I may not have redone the mission with the new fighters, so I will get right on that. 
. That said, the next mission will lack allied super capitals and put you in charge of a Thor class battle cruiser or a Posiedon assault carrier as well as some destroyers, making you a more integral part of the mission.