So I realize Cid even says at one point the heroes have a right to lay into him BUT THEY DON'T so I will stand up for the little guy instead.

This guy takes orphaned children with no place to go and raises them as soldiers. He makes them use creatures that force them to lose their memory which means at least two of them grow up to be mentally unstable. Due to stuned emotional growth or forgotten trauma with no closure, they are thus prone to flipping out or joining the evil side.

The true aim of Balamb is also hidden from its students which mean most of the SeeDs we see who go off to risk their lives are fighting for absolutely nothing. They don't know crap about time traveling sorceresses from the future or that the whole academy exists to defeat them. They go off and die in some meaningless borderr squabble and who cares because that isn't what the Garden is even for.

To top it all offf, the place is actually run by this guy.
(SPOILER)