Yeah; Mass Effect.
Hate me all you like for saying it, but the clumsy movement, floaty aiming, inconsistent and awkward cover-taking, dreadful enemy & squad AI, tedious inventory management, horrendous vehicle sections, indiscernible improvements upon level-up*, and having to pause the game every 3 seconds in a fight to make use of powers made for a game that was just bad.
But by god if it didn't also have a killer soundtrack, great story, some awesome characters & themes, and a universe so deep and well crafted that, terrible gameplay be damned, I lost myself in it anyway. I bought ME2 on launch day and I've pre-ordered ME3's collector's edition, so I can say with certainty that games with tremendous gameplay flaws can certainly overcome them with other virtues.
*This one's more of a personal preference. The difference between being level 10 and level 11 is unnoticeable, and the difference between being level 10 and level 15 is only noticeable if you dumped all of your points in one category. I prefer the less deep but instantly rewarding Borderlands style level-up system, where you can immediately notice and feel the improvement after you jump a level. I realize not everyone shares my preference here.