Well, if you want to make a memorable story, then breaking conventions is probably the most important factor because that's what people actually remember, in terms of how human psychology works.
Any story that follows conventions and fit into established patterns, blend with what is already being made, which means a lot of people won't see the story as memorable because it's competing with all the other stories in the same vein or pattern.
In those cases, which story wins out in the minds of the audience boils down to a much smaller and narrow set of variables that are much harder to control (character development, flow, rhetoric, choice of words, etc).
Also, it's worth mentioning that games, unlike books, present stories in a completely different way. It's not limited to writing. The story is presented with visuals, and with audio as well.
A rather conventional and tried scene where two rivals battle each other to death, can be completely forgettable in a book unless the writing is completely excellent, but it can easily be a really unforgettable moment in a video game if the art complements the scene, and you have a really good track going in the background.
People are much more forgiving of a story that stands out from the crowd, even when it isn't necessarily all that well-written, especially in a generally well-designed game. Whether you make your game stand out by building a story that breaks story-telling conventions, or by making a game that break conventions in terms of presentation.
FF7 is a great example of the latter. It suffered from horrible localization, a rather unforgiving pacing when it comes to the progression of the plot, and many game-play traditions that many today see as bad.
That being said, it took place in a world that stood out(and still does) from the vast majority of fantasy/sci-fi settings, it introduced elements like cross-dressing, gambling, alcoholism/drug abuse, prostitution, homosexuality, "fossil-fuel", terrorism, problems surrounding a privatized military industry, and much more, and it assaulted your senses with this insane color-palette and heavy synthed sound-track that really captured the time-period, which all made it stand out from everything else being made at the time.
The final showdown between Cloud and Sephiroth in life-stream (the one where you omnislash the **** out of him), is probable one of the most awe-inspiring showdowns of gaming history, despite being a completely ordinary and stereotypical scenario that in pure writing would probably be completely forgettable.
People have to remember that games allow us to tell stories in a completely different way from any other media.
We can deliver more dialogue and action in a much more progressive way because we don't have to spend time writing out the setting and mood. The music and visuals do that for us, and those are by far the most important elements in creating a memorable story sequence in a game.
A scene that has a good mood, and a strong set-piece can be the background of a completely mundane and otherwise boring scenario, and still make everything seem relevant and emotionally charged to the person watching/reading/playing it.
People like to think that it's what's being told that is important, not how it's being told, and that's not so strange when you consider how the human psyche works. But, in the end, everything boils down to basic, subconscious emotional reactions, and those are usually best influenced by the things that by-pass our intellectual filters and go straight to the heart-strings.
Don't take this to mean that I think writing in general is pointless when it comes to video-games, I'm just saying that the standard for what makes a story memorable and good in terms of a game, is different from that of a book because they essentially are very different, seeing as how many of the elements you express in video-games aren't expressed at all in books, or have to be expressed with additional writing.
Case in point - even if you made an RPG out of a Shakespeare level piece of writing, if it looked and played like Dragon Age, then it would still probably drown out with all the other Dragon Age-ish games.
Pick a mood, art-direction, musical direction to your basic plot-outline first.
Build around that, rather than attempting to write some Shakespeare and and then attempting to just force it into a game.
Secondly, challenge general genre conventions.
Don't end up burning down the hero's village, having the hero captured by soldier grunts he could easily defeat scores of in combat, putting the hero in a jail he has to escape from, putting a maniacal evil guy who plans to destroy the earth, etc. unthinkingly.
The reasons those tropes pop up into your stories so naturally, is because, in all likelihood, you've read so many stories containing those elements that they're firmly lodged in your subconsciousness by now.
Give a care, and see if you can't just pull a 180 and surprise people a bit.
