Hey, you're forget something... she did tell Logan that she loved Scott in X2...
Jean: i love him...
Logan: Do you ?
Jean: Girls flirt with the dangerous guy, Logan... but they don't take him home... they marry the good guy...
And when Logan kiss her, she backed away ( after a few seconds... I know... )...
And in X3, her feeling towards Scott appeared after her ( for me, Phoenix implanted this in her mind...) flashback, when she said ( for me believed...) that his was dead... and after that, with Xavier... her refusal to talk about it was clear...
In fact, I think that she cares deeply about Logan, but her truly love is Scott...
Dany