are we looking at essentially "bad ends" and darker more serious stories if we choose to back a faction that doesn't agree with the real life affiliations of the creators of the game?
The whole point of the choice and consequence is to avoid decisions with straight 'good' or 'bad' solutions. The different races will react differently to each of your decisions, and there is a story arc for each of the races (which will be comparable in quality / tone / content).
