I saw all that as excellent tension-building. I don't think the story was trying to hide the fact that the Flood was lurking in the dark.
Speaking of Evolutions, what's the deal with Palace Hotel? Seems like it kind of retcon's a bunch of the Halo 2 mission Metropolis. It wasn't a bad story or anything, I just think it was really weird to include a story covering a section we've played in-game and then change big parts of it. Kind of surprising, especially coming from Robt McLees.