[Mark Walton]

I was trying to think of a way to do something like this, and the best I came up with was:

Create many new racial techs which players are not allowed to choose.

Create Neutral races which use these techs.

Each tech allows immediate creation of facilities, components, maybe even hull styles which are:
not available any other way;
much more useful/powerful than normal starting tech (even advanced tech).

So, these AI's can create these wonderful features, but players can not. Players can negotiate, conquer, or steal the techs but can't make any more of their own. It may be that there is only one world in the galaxy with particular facilities.

I haven't got as far yet as designing the actual techs involved, just outlining the plan.

With this type of setup, there might be serious competition to be friends with a particular Neutral AI - protecting them from other players conquering them, etc.