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.
Right, I think the fact that it was so obvious and un-hidden just made it more frustrating to me that it kept being built up. I was just thinking "I get it! It's the Flood, there's tension! Just show it already!" for way too long.
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.