Epic knew they did a bad job on the first game's story, they did as good as job as they could to actually make it interesting. Regardless of whether you think Maria is foreshadowed or not, it feels far more important than most anything Halo does in the games. The second in a trilogy always leaves more questions than answers, or it wont be a trilogy, I expect Epic to expand on the Sires alot in the third game. Thats where Halo really dropped the ball, the third in the Trilogy really dropped alot of the story. They didn't expand on the Covenant breaking up, even though in Halo 2 there are Hunters and Grunts that fight by your side. The story felt extremely shallow and pretentious. Gears 2 was almost the opposite, deep enough to keep you interested, but it knew that it wasn't going to be the next Star Wars or Trek. I don't read the Halo books, so I can't comment on those, Im talking about the games only here.
Something On Topic- Halo Wars story seems far more interesting than the rest of the Halo games right now.