I do love the idea of a race builder. Personally, I'd like to put in some races like Avians and Draconians. However, I wonder if a race builder is actually a feasible concept. My guess is that we have to lean on the modders for more races.
As for assigning a custom leader to a custom faction, that can actually already be done. All you have to do is create a faction, then locate the faction's file on your computer. Open it up, and then add (or replace. I forget if there's a default line) the following XML code:
<SovereignUnitType>CUSTOM LEADER NAME</SovereignUnitType>
Now, the one thing to remember is that the Leader Name is the computer's name for him, not your name. So, if you created a leader named Joe, the computer will actually save it as something like Joe8673202_432. You should find the custom leader's file on your computer as well, and that will tell you the computer's name for your character.
Anyway, once you plug that line into the Custom Faction file, you'll always have the leader of your choice leading that faction.
Or perhaps you already knew that, and just mean that you'd like to be able to set a personal AI strategy for each of your custom sovereigns and factions. I can only agree with you there.