I went with Mass Effect 3. As much as the ending was... disappointing (though there I still enjoyed the vagueness to a degree), the overall game was a long, expansive journey that allowed us to say goodbye to the characters we'd spent two other games interacting with. And even though the original endings didn't show where they ended up, it was enough to get those final moments with them. Those last bits of character to see who they'd become.
The runner-up for me was Walking Dead. The story was great, the characters were well-rounded, and the atmosphere was pretty excellent. But there were parts that I didn't care for that much. And even though the last episode ended so brilliantly, the gameplay to me was somewhat dull and created a slow pace when things should have been very hurried. The beginning of the last episode comes to mind.
Dishonored would have been on there. But while the gameplay was excellent, I felt the story was somewhat bloated. It was easily most hurt by the fact the main character didn't ever get much of a personality. And that became all the more obvious when Emily was involved. You could make choices on what to do of course, but that didn't say anything about the person doing them.
And finally, I haven't played a lot of the games on there. I'm about halfway through Spec Ops, which is good but not quite GOTY so far. I'd have played P4G if I could afford a Vita, since I never was able to play 3 or 4 before. I've wanted to try Journey, but I haven't gotten on my PS3 in ages. Xcom has been one I actually almost picked up but didn't realize a sale ended that day. And... well, the rest are pretty much all down to not being able to afford them.