As factions in mods and, hopefully, in the main game will become increasingly diverse, I think it would be great if we could add "random" factions to a game we are starting. That is, instead of selecting a particular enemy, we select a questionmark icon (or several) instead. These are then replaced with any of the factions available.
Also, another cool feature would be if we could select teams for the factions at the start. For example, I might want to play my faction and Pariden versus a lot of empires teamed up against us. A "team" in this sense means that we start allied, we can travel through each others' territories and the team cannot not break the alliance (it should be possible to win conquest even when you and your ally remains). Shared line of sight would not be necessary, rather the "team" represents an ancient alliance formed before the world was broken and maintained after contact is reestablished. That way, you can explore the wastes and actually find allies out there.