Personal copy-pasta, GO!
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Mass Effect has, since it's beginning, been an experiment into the concept of continuitous player agency - that is, that players will have the decision to make large or small changes to the story and it's details as it progresses along it's narrative arc, and that these decisions will be respected over the course of the trilogy. This has been the expectation from day one and thus far has been the most successful of Bioware's forays into continuitous player agency. Dragon Age followed a similar idea thread but did not center on a central character which the player maintains agency over, rather it is a set of different tales and different characters placed in the same World Setting in which player agency has ripple effects on that setting.
One of the problems of course, with any game that focuses on Player Agency, is that the same thing will mean different things to different people. People have expectations based on 'their' story, and the way you avoid stepping on 'their' story is to maintain player agency and give them the free will to choose their outcomes. This creates certain limitations on you as the author - you must maintain contingency plans for every player agency point you provide. Certain narrative and organizational devices can make this much easier, such as a binary 'morality' system (paragon/renegade points) and condition flags (companion loyalty/approval). This allows you to frame the narrative arc that your players will undergo while providing the illusion of complete choice. While this form of Player Agency is by design limited (your arc of control is more akin to 180 degrees than 360 degrees of movement, if you follow) it is an effective way of allowing your players to exercise their agency over the narrative while still establishing a general story arc which you can follow and plan for.
Over the past three games Bioware has done what, in my opinion, can be considered a masterful job of faithfully representing the continuity of player agency, referencing player choices in meaningful and meaningless ways via datapoints. Mass Effect 3 was the penultimate example of this, borrowing choices from the previous two games to almost completly form the narrative arc of the third - that is, your choices have finally become the definition of the setting (wether or not you saved the council, the rachni, etc) influences the characters that appear and how events play out in these games. Mass Effect 3 is exceptionally well polished (barring some frustrating bugs and annoying UI and quest tracking issues) and represents the continuity nerds wet dream - a universe of their own creation, the punultimate choose your own adventure.
However...
In the last 10-15 minutes of the game there was an abrupt genre convention shift (more in line with the
metaphysical pulp sci-fi of the 1900's than the
Space Opera /
Military Drama we had thus far experianced), a fundamental violation of one of the tenants of the
Writer-Reader contract. This abrupt genre shift has left fans feeling disoriented, confused, and dissapointed - which swiftly leads to bitterness and anger. Their suspension of disbelief and expectations have not been adequatly serviced, and thus the ending causes the story of Mass Effect - from beginning to end, from 1-3 - to fail. Many are now observing plot holes and inconsistancies - those plot holes were always there, but were forgiven. However a bad ending damns a story, it causes a blowback in the reader where their tension and emotional involvement does not achieve
catharsis and they're left to take it out on the author.
And this is why, I, and many thousands of other individuals have been so upset by the ending to Mass Effect 3. Our genre expectations and player agency have been violated, the finale of the story is uninfluenced by the continuity of our decisions and follows an unfamiliar narrative trend.