Well to be fair, the endings to Mass Effect 3 are horizon events, representing fundamental changes to the political institutions and or biology of species. The easiest to work with would be the Reapers being destroyed, the hardest would be the synergy or fusion event and how would you portray a situation where the Reapers are controlled by Shepard? Massive lumbering devices traversing the landscape yet somehow not dystopian. Story needs conflict and conflict in these settings, would be very dystopian, the synergy event could be represented by a kind of cybernetic setting with the absence of consensus. Perhaps the best way to represent the massive changes in society would be to have a introductory set piece that demonstrates the changes in society and the utopian elements in each setting, with the particular advantages of each setting and then ejecting the characters from the utopian setting into something else. Because not being able to use 2/3rds of your cultural setting from the beginning of the game is not a good use of narrative resources.
Actually when I think about it, that is kind of what they did with the Citadel, but with one fixed utopian culture, to me the Citadel was as close to a utopian culture as writers from a secular democratic society could conceive, which by its nature includes conflict as part of its process. If we were from a more Authoritarian society perhaps our utopian fiction would include a more "great leader" format. Of course you could argue that the player character is a kind of "great" leader, the fiction of a non fallable character but there would need to be moments where Shepard is wrong to provide an argument against a "great leader" narrative. Arguably the Cerberus storylines in Mass Effect are an argument against a "great leader" narrative, most of the mystery is generated by the player character having an incomplete picture and trying to resolve conflicting agendas. Also many of the key scenes before action sequences involve a kind of collaborative decision making process. The endings of Mass Effect 3 have the protagonist as an almost religious figure, with an increased historical awareness and consciousness facilitated by the technology of the Reapers to make decisions in a "great leader" role creating a near Utopian society. It would be bitter/ sweet to revisit those outcomes and engage in critiques of the various Utopian societies presented. Can you imagine the player characters having to combat Reapers and agents operating from the sacrifice or authority of the Shepard character?