I for one actually don't like it when the AI takes control of a custom faction/leader that I've created in the past.
There are times when I goof around with a design or try something new. When I play a subsequent game, I don't want to have the AI messed up and ruining my game all because they have decided to pick your previous goof.
IMO, there should be a check screen in the menu where you can pre select which leaders and factions are to be made available for the AI's use. Doing that also opens up possbilities for the steam cloud (as much as I hate steam) because you then can gain access to all sorts of leaders and factions that other players have made public, sifting through the data and deciding which leaders and factions you want your AI to be able to choose from.
Until this is implemented, everytime I've tinkered with a leader or faction, when I am done with it, I delete it, because I don't want the AI to become screwed up because of decisions that I have made in a previous game.
This entire arguement can be made for the current AI factions as well. If I play a default leader and create my own units. There is NO way I want the AI to also utilize those units in a subsequent game, espcecially if I've deisgned those units to operate under specific conditions whereas the AI will not be aware of those conditions and will blindly use the units out of context.
Granted I can understand that the AI should be getting better off of the units that you are creating. All that I am saying is that the player should have the ability AHEAD of time to select which units in addition to the default units the AI has access to. Again, the steam cloud could be utilized here to further the experiance.
The control mechanism must first be made though.