For the mission 1
1 and 2:The mission is supposed to be everyone slaughtering everyone.Making the Splendid into a Deimos,would create more chalenge,but as far as i can tell,its better to make the beginnig ,,WE ARE THE GODS OF UNIVERSE",and then something happens and it all falls into water,like in FS1,you fight against underpowered Vasudans and then the shivans arrive and kill everyone.Alzaz is still in danger from bombers and crazy Loki pilots engaging the corvette.The mission is made for normal and higher difficulty,where wing of General-piloted Hercs is a threat.Wait till mission 6,that's real BOE type mission with enemies everywhere.
3:Iota is actually supposed to be uncontroled ship parked there,and the turrets are simple AI.
4:I didn't add more messages just because it is a short mission,and for the Jupiter surrendering-SLAUGHTER.
5:Rapier and other destroyer,the Liberty have special super subspace engines that take 2 hours to recharge,and that's the reason it jumped at that moment,not before cause the NTF thinks they can force allies to retreat,however since they fail,they send in a super destroyer.
It was actually supposed to have the Hecate along with its entire fleet jumping in,destroying the Hope,and then it would be saving the Venturer until it jumps(what it wouldn't be able to).But i decided to make next mission hunting the Hecate.
For the narration,same as the above.
If i do a remake of the CZ,which i may do after releasing the FD,i will follow your advice to make it better.