brian reed said in an interview that mar-vell's story is much more complicated than just a secret invasion tie-in. for example, if mar-vell were to die in the present, while time-displaced, he couldn't get back through time to die in the past, thus causing paradoxes in the history of the marvel universe.
in issue two,
Spoiler:
mar-vell's clearly asking about the presence of skrulls, though it's not clear whether he's on earth, or these visions are from the past, or from another location such as kree space.
There was an spoiler about what happens to Captain Marvel in Young Avengers Hulkling Mini, do not click in the link if you don't want to be spoiled.