Honestly? I think Bioware's grave mistake was trying (and failing, some would argue) to break the Illusion of choice with the branching endings. Deus Ex: Human Revolution had this same issue in my opinion, only it worked just 'slightly' more in the case of DE:HR than it did in ME3 as the endings didn't have as dire consequences and on such a scale as that of ME3's. . .what's more, an ending (the pro-chrome message) is confirmed canon by the developers and is what the upcoming Mankind Divided is based upon. Firaxis, makers of X-COM 2, also took the most seen ending in X-COM Enemy Unknown/Within and made it canon for the next game. . .only that ending was the Game Over screen. That's right, they canonized you failing in the first game! What a twist! 
Both of those games simplified their options by canonizing the least destructive ending for the setting: The other two endings (not counting the 'screw the endings lets just drown everyone option) in DE:HR would have hampered the setting given its heavy augmentation bent. Meanwhile, canonizing defeat in X-COM Enemy Unknown/Within makes for a more interesting narrative than 'Oh we won, but then the aliens came back'.
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I would have preferred Bioware just having gone with a simple 'Boss Fight then Push Button to End Reapers' Ending, and then, just as we did in the now uncanon slideshows of Dragon Age: Origins (A game where, you know, you had two option variants leading to the same ending type. You didn't get the option to become an Archdemon or or turn everyone in Thedas into Darkspawn-Norm hybrids.), the player gets to see the consequences of their actions:
- Do the Krogan move for peace or war? If Peace, are they rewarded for their efforts with planets to colonize and a seat on the Council? If Wreave was Chieftain, are they stopped or brought into a civil war because of Bakara, or do the Krogan have to be fought once again? Was the Genophage sabotaged while either Wrex or Wreave were chieftain? How did that affect things?
-What of the Rachni? If war happens above, do they come to the aid of the council and fight off their old enemies, the Krogan, or do the Rachni, led by the Reaperized Clone, fight the Council as well?
- Does the peace between the Geth and Quarians last? If the Geth were destroyed at Rannoch, do the Quarians earn an embassy on the Citadel, let alone a seat on the Council?
- Does the Council continue to trust the upgraded Geth even after they help fight the Reapers? Based on the Survival of The Shepard's squad and the actions they made, the Geth could withdraw back behind the veil or stand alongside the council as equals.
- What of the surviving Batarians? If the Terminus Fleet came to the aid of the Council, are the Batarians given an embassy and colonization rights to find a new homeworld? Or were they cast out just as before?
- Keeping the readiness and/or EMS score, how long does it take the races to rebuild their lives? Do wars break out after planets are too damaged for re-colonization? Do limited resources and garden planets cause strife between worlds? Or are they able to hold together and rebuild, perhaps not as before, but with Unity and hard work they prevail?
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A singular ending with modular variants would have been far more preferential to three endings that everyone complains about. . .but I still hope Bioware canonize's The Shepard's death in Mass Effect 2. . .you know, before they became 'The Shepard' and thus aren't even worth mentioning in Andromeda.