Bioware should remove decisions from the game as it leads to compromises within the story and prevents a really good tale from being told.
Hm. Don't think that's possible. Bioshock is one example, but SpecOps: The Line is another. Playing, or not playing, the game is also a decision.
What they should do, however, is sit down and decide what themes they want in advance, and then stick to them. None of this Geth pinochio crap after having established the 'we are different, and are cool with that.'
They should also go with thematic morality, rather than tone-based or good-evil. Don't just switch what Paragon stands for just because it's suddenly nice to commit perjury when it's nepotism in your favor.
Should they give us an Asari squadmate who is like Captain Enyala?
Dead? I don't think that'd do much.