I wondered when in particular Sins of the Prophets fits within the Human-Covenant War. The time of Halo 3 seems to match SotP best, in terms of gameplay; there would be no 200 Super MAC guns, which would in-game make Earth almost invulnerable, and no UNSC Home Fleet that would actually overpower the Covenant invasion fleet in-game.
As I compiled space cutscenes from each Halo game, I noticed the Unidentified civilian transport craft from Halo: Reach. I remembered the Battlestar Galactica re-imagined miniseries and the subsequent first episode, watching Galactica fight to protect the escaping civilian ships. I also remembered playing the free game Diaspora: Shattered Armistice, and feeling the intense purpose in fighting to buy time for a civilian ship to rendevous with Galactica.
Finally, I recalled playing the Enhanced 4x Mod for SoaSE and thinking, "The only thing this mod is missing is more civilian ships." I realized that I felt more civilian ships would complete the SotP experience as well.
I know that technically, for the UNSC in SotP, civilian ships exist in the form of the envoy cruiser, the colony ship, and the trade and refinery ships. However, I feel that including the Unidentified civilian transport craft from Reach would add to the SotP experience, with the presence of large civilian spaceships for players to defend.
I don't know anything about SoaSE design, except that its hard-coding is moderately restrictive. I thought of 3 ways that the civilian ship from Reach could be included in SotP:
1. Replace the ONI Sloop with the Civilian Transport Ship. The ONI Sloop is used to only scout planets and occasionally reveal and destroy mines, as its small pulse laser is "utterly useless." The Civilian Transport Ship can fulfill the same function, even if it reveals mines through being destroyed by them.
2. Add the Civilian Transport Ship as a capturable NPC ship. Although it may seem superflous, the player arriving at an NPC-controlled planet and recovering an unarmed, helpless civilian ship could be an enjoyable experience.
3. Add the Civilian Transport Ship as a capturable Pirate/Flood ship. The idea is that when Pirates (Flood?) attack a player-controlled planet, Civilian Transport Ships will be used. Again, if the player could recover these civilian ships, it could make the whole battle more fun, even if there are no economic benefits to having a civilian transport ship, unlike the trade or refinery ships.
I know that these may be far-fetched ideas, but I honestly feel that the inclusion of more civilian ships in SotP will make the experience feel more populated and purposeful. In any case, if you've read all of this, thank you for entertaining the thought, and thank you to the SotP team for a spectacular mod.