Yes. A good story and good storytelling are two different things. One is the message, what's being said, the characters, the plot, the themes. One is the execution, the dialogue, the pacing.
George Lucas comes up with good stories, but he himself is a crappy storyteller, unable to craft dialogue to save his life and far too concerned with selling toys to show us action that actually matters as opposed to wasting our time with extended commercials for his merch. Choices in execution make it unclear as to who the real main character is in some of his works, particularly The Phantom Menace, which, if you follow the formulae in the Hero with a Thousand Faces, actually turns out to be Jar-Jar Binks rather than Anakin Skywalker--Anakin being the actual hero and getting considerably more time with the reader if you follow the books instead.
Mass Effect is a good story poorly told as well. 90% of the dialogue Shepard has is just questions, making her a very flat, one-dimensional character; a mere puppet for eliciting exposition rather than a hero facing any kind of struggle or expressing any desires. It's interesting because of the novelty of making choices in the narrative, but there's very little sense of actual characterization on Shepard's part. She comes off as a walking stereotype rather than having actual feelings. I can say this of practically all of Bioware's player characters. Their one strength is when they present players with dilemmas between the other characters' interests--which tend to be one-note and very predictable when it comes to dealing with them in gameplay, though they make up with it with a few interesting turns outside of gameplay. Miranda Lawson's insecurity in spite of her genetic perfection is a great character trait, which I wish had been explored more. Mordin Solus actually turns out to have a broad variety of interests. Et cetera, et cetera, et cetera. And of course, occasionally outlier characters like HK-47 and Minsc show up who just steal the whole damn show because they're so entertaining. All Bioware's games have an underlying theme of authority and what's best done with it, but they seem to skirt around it a lot.
Final Fantasy 13 is a good story told poorly in COMPLETELY different ways. The themes are there. The characters are POTENTIALLY sympathetic and POTENTIALLY have interesting struggles. The setting is intriguing. However, every cutscene is a total waste of space on the disc, every line of dialogue is pointless gibberish, and the game seems to be TRYING to withhold any detail on what's going on or what the world is like. When it does get to expositing it tries very hard not to involve the player in the interesting parts of the story, incorporating them as flashbacks, which makes them difficult to care about. It's not so much telling its story as wasting the player's time while going "honest, guys--we'll tell the story soon." It also changes its mind a lot on what tone it's trying to set, failing to maintain gravity. Its twists are predictable, and the lead characters are clumsily shoehorned together because the developers couldn't find a way to introduce them smoothly or gradually.
Likewise I've seen weak or mediocre stories told well...
Uncharted 2: Among Thieves really has nothing to say, but its dialogue and fleshing out of the relationships between characters are commendable, its use of historical content creates an immediate connection with players, and it knows how to execute its big twists frighteningly well, turning predictable re-uses of tropes from the first game on their heads and actually managing to surprise me. And of course we've all heard the reviewers gush about the amazing scripted events.
Call of Duty has been praised to no end for its storytelling, but as anybody should know it's Michael Bay-style military fiction ultimately signifying nothing. Russian terrorists? Really guys? Those people who've expressed no interest in fighting the United States for how long now? You're about 15-20 years too late. Tough for me to see a point in exploring that relationship. Yet, like Uncharted, recent games in the series have managed to stand out with scripted events, and you have to give its makers credit for not being afraid to pull their punches with certain events. For many, the sight of America being invaded or terrorists tearing through an airport was more than enough shock to give it some significance. They also have the notable distinction of giving the British a strong role, recognizing there's countries other than the United States out there who are worth mentioning. On an artistic level it's junk food, but on a technical level it knows how to make deliver a punch.
I would say good storytelling is more important. A message that's not executed well is as tiresome as not having a point at all or as annoying as being beaten over the head with it, and if I can't have both I want to at least be entertained. But I'd PREFER both, and have ignored games (like Call of Duty, as a matter of fact--my opinion on it here is hearsay) for not having anything for me to grab onto.
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