(Spoilers of course)
Frankly I worry a little about the story itself. It was actually pretty interesting, however the narrative is haping up to make all the factions as antagonists. To be fair all of them were always *** in the lore, so they were nover portrayed as wholly good. But there is a problem with setting up the questline to make all factions eventually your enemy.
The problem is that during the many years of no-story gameplay many players grow fond of roleplaying into a faction or another, despite their flaws, and if the story really is shaping up to make you carve your own path, I bet it will dissappoint a lot of players. Personally I'd enjoy it more if you could choose on faction to support (or not supporting any) during the game.
Basically doing the exact same Galatia academy quest, but having to ally to one faction to support the academy.
This could make each gameplay slightly different. Going for tri-tachyon gameplay? You will not fight the phase fleet, and it was in fact tri-tachyon whole idea to send you, a disposable captain, to see what's up with the alpha site.
Luddic church? Add extra dialogue where you can choose to say you're a undercover agent since the beginning, to reap the benefit of this for the grace of ludd.
It's not necessary to remake the entire questline from scratch, it will require some work, but just giving a few different quests, adding a few different lines could make it feasible for you to actually choose a faction. I think a lot of people grow fond of choosing a faction to support during gameplay, and maybe there will be some narrative dissonance if we really have to pick fights with all the factions.
Even for things like our capital manta ray narrative solutions could be found, we know that all factions want to study that thing, but no need for the faction you support to get pissy with you.
just a few examples that I come up with on the spot
Tri-Tachyon: Of course you can stay with the xenorphica... we aren't actually sure it's safe to pilot it yet, but if you want to test it for us... as long as you keep sending reports and making some tests for us. Also, It's more politically beneficial that the ship is not directly connected to us.
Persean league: Look, we decided that you should better keep the ship... we are afraid of a... political power inbalance if one or another of the league core worlds keep the ship, and to avoid conflit it's better someone that is loyal to the league as a whole to pilot it. It will project force for the league, instead of causing in-fighting.
Sindrian Diktakt: Im gonna tell you the true, this is extra-official though. Andrada knows how dangerous it is when your own faction tries to cut short the career of a rising and charismatic Captain. He don't want you to give you any ideas about rebellion, also, he understands the importance of heroic figures, and you're shaping up to be a heroic figure for the Diktakt, my friend.
Luddic Church: Oh no, no no no. We cannot touch that tool of Moloch. You captured it from the belly of the beast itself, Ludd has choosen you to use this abomination, you and only you can touch it without being corrupted by it's power. Until the right time to use it for the cause of Ludd.
Hegemony: We wouldn't trust you with this missions if we doubted yout loyalty, but our trust is not blind. For your pristine service record, you can keep flying the ship, but for the cause of the Hegemony. The High hegemon came from the very botton, just like you, so he favours your work, you conquered the honor of using this ship, captain, don't squander it.
And to top it off, each faction could give you a different officer companion that doesn't count for the limit of officer, story wise he is there to watch you closely and see that you remain loyal, but gameplay wise he is another reward. Could even make him sometimes give opnion on the questline, as a more active fleet member.