I'm quite happy with the way the faction interaction is designed, with control being exercised by activity rather than by top down decision making. This requires a more pleasant (if more challenging) style of group leadership in which one has to provide common goals, interesting objectives and fun activities that your group will engage in willingly. If the group wants to do it they do and if they don't they don't - its kind of like a group decision mechanic. I don't think having a single "leader" autocratic system would work for us.
Also for clarity, it is not only elections where the extreme faction-wide effect is imbalanced. In combat conflicts, most mission effects are negated. Where there is a popular mission running location (skimmer stacking, smuggle stacking, close to engineers) during wartime the ruling faction also gets hammered as missions run for them do not count.