Mass Effect 2 was hands down the best game on that list. Not a single character in Skyrim can hold a candle to the Mass Effect characters when it comes to believable, interesting personalities to interact with. Too bad ME3's ending and starchild character ruined the series' good name.
I'd place Portal 2 in second, Bioshock third.
Not surprised to see Skyrim at top though, it just has a certain mass appeal.