I thought the story was supposed to be darker than the SCII trilogy (that's what I'd heard) but so far the presentation's still pretty silly. It's not surprising they chose to make Nova the main character since she's probably the most compelling non-main character out there and also this will appease the people still pining for Ghost.
Spoiler
I'm going to reserve opinions on the actual story for now until at least the second mission pack comes out, but I don't have any actual problem with the Psi Emitter thing going on with the Defenders of Man, I guess.