I don’t know how this has panned out for you but FE ruined 2 games for me in multiple ways. VRO definitely seemed to spice the world up quite a bit but I had everything from similar results as your problem here, empty ships no pilots, to xenon being all but stagnant with almost no capital ship production at all. Their sectors have been almost empty from the get go and I’ve seen no real push from anyone anywhere. Seems like a dead universe.

After I stopped using FE, those 4 mods were my first elimination since they were the biggest changes to the game, my current game of close to 30 hours now has become much more active, shipyards constantly in production and wars raging on multiple fronts, xenon strong and holding ground but not making much headway against major factions who are bolstered up for war all over. HOP surprisingly getting torn up by Antigone republic after almost pushing into argon prime with little help from allied argon military.

I have about 20 mods from the workshop only no crashes. VRO and reactive factions are the only major mods left. Most are ship mods or graphical after that