Yea, honestly, denying her screentime and making her look bad as a leader doesn't really help. I never really saw Hayate as suited to be a leader either (
section 9 leader she is not!); just because you have the power doesn't really mean you need to be one. She probably would have been better in a advisor/ambassador role. Chrono would have probably been better suited as a leader; I seriously doubt he would have let the headquarters get sacked. Well, I suppose he kinda just collected dust with his fleet.
I probably disliked it because it just felt they couldn't give her anything to do.
So I hope we can fix things here.
edit: Chrono too! Give him more stuff to do...