I think the situation with stuff like Dan's Gears of War review or the reviews of Deadly Premonition are, do you give a final score based on point-to-point factors of the game, or are you giving that score as an overall representation of the good (or bad) experience that you had with the game?
One great example for me is Lux Pain on DS. The English translation was horrible, and if I just went down a list of points, gave each a score, and then tallied a final score, I would be giving it a lower score (let's just say, for example, a 5 or a 6). If I simply scored the game depending on how much I enjoyed the experience - beyond its good and bad points - I might give it a 7 or an 8.
Some of my favorite games ever have horribly broken aspect to them. Silent Hill 2, a game I adore, is really kind of a shitty game if we're being honest here. Same with the original, which I also love dearly. I spent a ridiculous amount of hours with Phantasy Star Online, but man that game was a mess in a lot of ways.
So, you know, I can totally understand how you review Gears of War, point out a lot of flaws, and then give it an A+. I think what's direly important, though, is that your organization have a standardized decision on that. I have the feeling that 1up wasn't that way, and they were more "the score is the final grade of all points" kind of thing, so that's where something like that Gears of War review can feel so off the mark.