I am not in the target audience, I think. I review story last. I have one rule though, "if you have a story, make it functional at least." The problem is many fail at this part and I don't have mercy for them. This is why Super 8 is awful and Avatar is amazing for me.
I enjoyed Limbo. My thought about the boy was very different from yours though. But I think that's the beauty of Limbo's story, it is open. I also enjoyed the length. My saves from Bioshock are scattered from 2008 to 2011, I finished it last month. That's long, I had to show great determination to finish it! I enjoyed Half-Life 2 episodes more than Half-Life 2 because of the better length too. And I fancy my played-in-one-sit games.
I didn't like Bastion from the short demo I played. Because the gameplay is kinda repetitive. I just can't play that kind of game and listen to the narrator at the same time. It is distracting. Funnily, I would love to see the same narrative in my Skyrim journal.
Here some games I liked their story.
Final Fantasy 8:
Exploration was rewarding. I can control the pace and I can freely roam a world... Constantly encountering new settings and characters and gaining new spells and abilities through the game kept it fresh until the end. I also liked the interactive cutscenes.
Undying:
Constantly encountering new settings and characters and gaining new spells and abilities through the game kept it fresh until the end. Again?

Funnily, I was frustrated by this game at first, I thought "I stuck in this boring mansion for eternity". I didn't know.
Silent Hill 2:
A whole town and a mind for exploration. Slowly uncovering the mystery but not all of it.
Myst III: Exile:
Exploration of different ages and puzzles.
Jedi Outcast:
Rich settings in Star Wars universe and fun gameplay.
Dead Space:
Gameplay is fun, atmosphere is solid. It is closer to Silent Hill 2.
Max Payne 2:
Gameplay and atmosphere.
Prey:
Gameplay and atmosphere.
I purposefully avoided reviewing the stories, characters and such. So I liked a story, no big deal! I like many stories which you may not like, or vice versa. I think the key point is why I sit through them. So I listed those whys above instead.
And Morrowind, I think it is worth noting this exclusively:
It is an open text. There are so many viewpoints in the game world, you can adopt one or have your own interpretation freely. While it is a linear story, it gives so much room to player. In contrast to Limbo, the power comes from the complexity. There would be so many different answers to the question "why did you do it?" about Morrowind's story. It is almost wrong to call it a story, it is something else because player agency is still, somehow, seemingly intact.