Communications and diplomacy could use some realistic timeframes, especially for some of the civilization-specific mission arcs.  For example, in one playthrough, my Vaulter civilization was on the far side of my huge galaxy, on the other side of Craver space, from the Auriga the mission assigned me to find.  It took 28 years of travel to find, and 18 years to return to my own space.  But as soon as I search the Vault of the Endless, not only did Isyander (and I had never even heard of him or the Academy up until that point) contact me, but his minions managed to show up in what I think is supposed to be my capital and met with me, to offer to trade me for my robot for some ancient telemetry from my ark ship.  By that time, I hadn't found the Academy yet, and I'd only met the Cravers, who were still decades away from reaching my home systems.  Now, I get that Isyander probably booby-trapped Auriga with probes or whatever and he probably had ample time to study the ruins, translate my language etc, so he would've known I arrived and developed the means to communicate with me, and, as it turns out, the Academy was only 5 or so units of travel away from it (on the other side of where I came from), but how did he manage to reach me, basically immediately, on the other side of the galaxy, in less than a single year?  It seems to me that the game coud benefit from missions that respect or tested for distance (and prior contact) a bit more.