I think there is a really fine line between giving bad outcomes and offering the player choices.
For instance, ME3 dictated the exact order you went about the missions at hand, to the point where you could never get to Thessia on time. This gave us a forced defeat that we have no way of averting, which our character is forced to feel bad about, despite what the player may desire to their character to roleplay. If, instead, we could choose the order of planets we choose to help, with a forced defeat happening on the last planet we visited, this could serve to be more palatable and make the player truly FEEL as if it is their fault that the planet was lost.
As an example, if you could visit Thessia and Tuchanka first, you'd be forced to visit Rannoch and see those forces fall to the Reapers. Players could still wind up choosing Tuchanka and Rannoch first, because, say, Krogans and the combined might of the Quarians and Geth are worth more than Asari commandos in terms of the war effort. But, on the other hand, maybe a player that wants to not cure the genophage leaves Tuchanka for last, such that the loss of the Krogan is not nearly as big of deal to them, philosphically (but that may mean the overall war effort may suffer).
This is, to me, excellent choice and consequence, since it gives the player hard choices, it offers dark outcomes regardless, but a player can instill their character's morality and philosphy into those choices and, at the end of the day, be comfortable with the "dark" outcomes. And, of course, there will always be the "I'll do what is best for the war effort" approach, securing the strongest and best forces and putting their own feelings of morality aside... that would be the true distiallation of the Renegade concept.
Now... whether or not the resources exist to pull this off is a different question. But I think it is a good goal to aim for, if possible.