... what obviously came out wrong, but only in the superficial aspects. I don't want to view Henry as perfect; I simply object to many of the detractions for, in my opinion, wrong reasons.

Besides the fine arguments advanced by Tom, Robbin, and Reeba, I see things differently from you and others in that what you call weakness in dealing with his father, I see as recognizing that he can do nothing about his behavior -- simple, proper prudence combined with filial respect. What you call justifying Frederick's behavior with Isabella, I see as recognizing that he has no power to influence him. Indeed, although he doesn't spell out in words his disapproval, he makes it clear when he talks with Catherine (ch. 27):

"Then you do not suppose he ever really cared about her?"

"I am persuaded that he never did."

"And only made believe to do so for mischief's sake?"

Henry bowed his assent."

I can think of no incidence of Henry's speech or behavior that can't be (in my eyes) better interpreted as prudently accepting what he can't change, or even influence, and/or guiding Catherine -- not pressing her -- to better understand herself and the new world around her.