Just remember to keep in mind that it's Rob's Top 5-- not an RPGFan top 5 or an 'Overall, all time Top 5."
This. I'm not arguing that Rob made bad picks, just that if we all got together and wrote up lists of stories we were disappointed by, there'd be some doozies, and it'd be a long list. :)
Of course, the other aspect of "underwhelming" is that it carries the assumption that you thought a game would have a good story, but it didn't. For example, Fallout: Brotherhood of Steel has a story that is stupid and terrible and doesn't fit with the canon Fallout universe. But I wouldn't call it underwhelming, because I didn't expect it to have a good story.
Edit: Looked at my list of scores and was reminded of White Knight Chronicles 2 and Paper Mario Sticker Star. I would say that both of them have underwhelming stories. WKC2 appeared to be this big, epic thing, but the developers didn't seem to think that its story was even worth telling. Paper Mario: Thousand Year Door had an awesome story, and although it wasn't much of an RPG, Super Paper Mario had a good one as well. Sticker Star, however, felt like it had a story almost as an afterthought.