It's not exactly the new story or characters that's the problem. They are taking a well developed and loved series, and shifting to another play style. They've made an RTS that people love, but that doesn't mean they're capable of making a decent shooter. Fitting the systems that have worked in the RTS into a new playstyle might not work. And no matter how pretty it looks right now, I don't think you should get your hopes up yet.

And, yeah, you don't need to tell me about the vast lore behind the Warhammer 40k universe. Though I've never gotten into it, I work in a bookstore, and I've seen that section.