Egosoft goes with the terrans because the first protagonists of the X-series were terran (Kyle from XbtF and X-Tension) and half-terran (Julian from X2/X3R). To essentially "end" that story-thread, they had Kyle find his way home.
Look at it this way. The terrans after the destruction of the warp-gate are essentially a culture entirely based on post-9/11-esque fearmongering dialed up to eleven. And that kind of trauma-induced fear isn't exactly easy to heal, and as something irrational, is hard to judge from the outside.
Almost a millenium of constant whispers of a threat nobody alive even remembers anymore plus outlawing any research on that matter. A perfect growbed for an entire solar-system full of grown-up teenagers that want to hide in their room for all eternity and can only answer a knock on the door by barricading it.
I've edited my initial post - credit where credit's due.
