Thing is, how would she mean Jean, though? Would she mean Jean is in a position to thwart her plans with Jean having a team plus Wakanda and Atlantis backing her? It can't mean that she's afraid of Jean as a psi because that would be PIS so bad. I think Storm makes the most sense here.
Even at the end of issue 1, Nova doesn't seem scared at all after she tells Jean that she's no threat to her without the PF.
http://2.bp.blogspot.com/-Ct2UU2DG43...600/RCO030.jpg
http://2.bp.blogspot.com/-6U7BLYYS2m...600/RCO031.jpg
Though, she does seem annoyed by Jean's interference at the UN:
http://2.bp.blogspot.com/-r2Lpn9g2aZ...600/RCO028.jpg
However, that's not fear. The fact is, why would Nova even make the effort to hide herself while entering the mansion if nobody there could pose a threat to her? I mean, Ororo is the only X-Man around right now that would give Nova some serious problems in a fight.
So, I think she sees Jean as an annoyance, but feared Storm when she went to try and get Ororo under her control, hence took a very sneaky route to reach Ororo and catch her off-guard while she was sleeping.
Well, anyway, that's what I'm getting out of it.