Well, I do think that Bioware's felt need for "one-size fits all" villains has gotten them into trouble in the past. For instance, I've always suspected that the main reason the Reapers are so powerful and so insistent on destroying all intelligent life is that this gives Shepard a reason to oppose them no matter his or her moral alignment. Even the most sociopathic of Shepards will want to prevent the Reapers from wiping out the galaxy because after all, that's where he keeps all his stuff. Thus, no matter your alignment, the game can funnel you into its basic plot without the need for significant branching.
Maybe something like a TW2-esque branching paths system could work here; for instance, you could work for characters A or B; if you work for A, your villain is B, and if you work for B, your villain is A. Creating your own villain altogether seems unrealistic to me (what if you created an inept villain? How would that work for the plot?), but allowing more flexibility in terms of who you are fighting against may give you more freedom to define the personality and goals of your character.