Here is my 2-cents to chew on.

One of the problems that complex turn-based strategy games have is a sometimes steep learning curve. So, the more detail you put into the controls your player has over their empire, the more intimadating it can be to new players. One fairly obvious solution I don't feel I see enough of - is tying empire control to whatever tech tree is used so as to more slowly introduce more detail as the game progresses.

For example, think about starting your game with all or most of the control tabs you mentioned (agriculture, diplomacy, etc.) either very simple or locked. Then slowly unlock features and add more detailed control based on tech tree milestones. Something like "agriculture mgmt" as a tech to unlock the tab and expanded controls for subsequent techs (quantum agricultural mgmt, alien-hybrid farming, etc.)     

I think the goal should be that the player doesn't need much instruction to get started and the complexity of the game is revealed by progressing within the game. You may have already thought about this but I think an overly complex early game is the number one mistake most strategy games make.

Also, to avoid the problem of overly weird hard to pronounce alien race names. I have always thought it makes sense to name them from the presepective of the humans (terrans). Sort of the way that many real Native American tribes are named from the perspective of another tribe (i.e., "the people that live in the hills", etc.).

Along those lines, maybe think of alien race names like: "The Silent Ones" for the Filoj, "War Weavers" for the Mongyr, "The Favored" for the Vatragyr. These types of names make it easier for players to distinguish the races and fit into their backstory.