Well, I can see some sort of "it was one of the ships that made it" given the EI might not have initially realised that they were going to take over 50% casualties in transit into the Paradiso system. But it was totally unmarked as civilian in an otherwise totally militarised area.
I know Infinity is heavily informed by anime tropes, but can we please skip the Harem storyline? Remember that the Shas racial priority is "Do whatever it takes to survive" Dropping a seed ship in a war zone could help provide reinforcements (which would make it a valid military target under current Laws of War), and it's possible that the EI usually stomps the opposition hard enough that nobody had the capability to destroy a seed ship by the time the seed ship arrived. (Remember, 50% casualties in transit)
I don't know. There's something fascinating in a story of how Thamyris brags about being the lover of the Human Sphere, only to hear "Ekhm, actually..." from Angus... No way it's going to be Aida. In a classic Betty and Veronica plot Boring Betty (Bipandra) usually wins over Vivacious Veronica (Aida, and actually all the other girls). I don't like it, but that's the way writers usually go.
Given certain changing tastes in the anime industry, my bet is on a surprise last-minute seduction of Achilles.
I mean, people were wondering how Sheskiin got close enough to scan him. He clearly has a Kirk-complex, loves the green skinned women.
Angus ends up seducing Achilles but in a surprise plot twist achilles is actually Patroclus!! Angus will be able to get over the deception because he actually has a secret as well...Angus is actually Achilles.
Of course we then have the spinoff where all the characters are students in high school and all the girls just want senpai Angus to notice them.
Perhaps just a difference in interpretation. I read it as the EI isn't totally happy with the Shasvaasti as their Transcendence project is going nowhere and it feels they are a little too distracted with their own agenda. It's nothing major at this stage but CB are painting a picture of all not being 100% rosy in the EI garden and the EI not bring above replacing it's client species if it feels they aren't doing their job. Basically giving themselves narrative scope for future shakeups in the future should they wish to.
I have a hunch that the EI will propose to Aleph. At first she will say no, but in the end, AI (which is also the word for Love in Japanese) will conquer all. Aleph and the EI will join forces, and call themselves "Alei". Then we will have a new Faction called AI Allied Armies (A3), composed of PanO, Yu Jing, Aleph and Combined loyal to "Alei".
It's no use living in denial. When Aleph and the El finally get over their anime romance comedy hangups, at the end of season three, all of your sectorials are going to be discontinued.