Any story will sound unique if you describe it in painfully intricate detail. I'm not going to argue much about whether or not you think Halo's plot arch is conventional. "Super soldier must save humans from alien invasion/ancient doomsday weapon" seems a relatively plotline to me. The most interesting thing about the story, given our current social context, is the fact that the aliens are religious fanatics. Unfortunately you wouldn't even know it in Halo 1 unless you read the instruction manual -- kind of a failing on Bungie's part. The "Your destruction is the will of the gods" line from the E3 2000 trailer ruled, but then the final game comes around and the Elites don't even speak English and nobody ever seems to make reference to their goals or religion. Just looking at the Halo 2 commercials though, you can tell they are fixing the problem.
It would seem to me however, that the execution of the story is entirely conventional. Minor radio chatter to relay changing mission objectives, 2-3 minute cutscenes between levels. They're not making any kind of important stylistic leaps, or trying to really integrate narrative and gameplay. They are pretty much in the same place where games were with Tomb Raider 8 years ago.
To be fair, the HowStuffWorks seems to be caught up in the "Oh boy, movies and videogames are about to mate and have children" sentiment that ruled the Playstation generation, so I suppose it only makes sense that they should worship the style that developed then. I get the sense however that they haven't played much else, and aren't really used to writing cogently on games.
And if the backlash-rumblings about the conclusion of Halo 2 begin to to pick up steam once the game is fully released, I think you are going to see some very major questioning of Bungie's storytelling ability in the near future....
