I'm disappointed ME3 won. It was a good game all the way through (I liked the end) but it does not compare to The Walking Dead or Spec Ops or Journey.
Imagine the writing wasn't bad(along with very very good bits) all the way through, that most of the exposition hadn't been told through three people standing around a table and that they'd given you a reason to care about earth other than it being Earth. Then it still isn't game of the year material because it didn't using it's gameplay innovatively. Here is a question, what do the RPG mechanics convey in ME3? In KotoR and KotoR2 they were about powerful people slowly rediscovering power from isolation and represented an increased connection with the force. In Planescape levelling up was about becoming stronger as you understood your person. In FFX levelling was about Tidus growing more used to the world and more capable in it (FFX is a great example because each characters ability in battle reflected thier personality, Auron was a heavy hitter, Wakka a fun loving guy taking down lighter foes, Yuna a healer, Rikku couldn't fight well but was fast and had flexibility). Even FFXIII understood this and levelling was about giving in to the Fal'cie and excepting more of their gift.
But in Mass Effect? Levelling is just a thing that games have.
Whereas The Walking Dead and Spec Ops understood everything about their mechanics, what every choice, every hint, every screen flashing red meant and used it to enhance their goals and the narrative.
I reckon ME3 won because more people played ME3 and most people won't vote for a game they haven't played