The problem is Rahphexon is that you are not beat over the head with it. In fact, I don't even know how you would interpret that to be the case. In ME1, we are presented with basic lines of the genophage story (fairly black and white); in ME2, the details are expanded and, through further exploration, we are allowed to see where the nuance is.
The genophage is not the center of the story, so it is not constantly being repeated or molested in conversation after conversation, like the Focus and L'Cie/Fal'Cie crap in FFXIII. Indeed, the genophage mostly comes up in conversations with Krogans and Mordin, which is logical, since one had a hand in sculpting a modifier to the genophage, and the other is the race who was its test subject. Nonetheless, Krogan and Mordin scenes do not even take up 10 percent of the game.
The problem is what you're doing is WISHING they're equivalent. You're wishing that you can justify the badness of FFXIII's plot and characters by dragging a game which is clearly, indisputably superior in writing and characterization, because it makes sense in some point you apparently think you have.
I can, however, list actual substantive reasons why the writing of FFXIII is bad. You seem incapable of giving examples of "being beat over the head", instead choosing to focus on vague problems with game having moral ambiguity. As if moral ambiguity is a problem, something the game chooses to lord over its fanbase as if a pretentious aristocrat!
It's ridiculous. You should just admit you have a problem with moral complexity, and are incapable of distinguishing between bad writing and good. If you were capable, there is no feasible way of saying ME2 and FFXIII are equivalent on this level.
Gameplay wise, sure, that's open for debate. Writing? No.
