is it a problem that all the various organizations in battletech are near uniformly morally detestable? I don’t think anyone is positively depicted outside of stories told from the perspective of individuals in the organizations, who of course view themselves favorably.

You’re definitely not wrong. Admittedly my days of owning boxes of miniatures is long over, so my battletech knowledge does not extend beyond the late 2000s. Maybe it’s even worse now. Not to mention any sort of narrative lore controlled by a big business that hires working writers to fill out plot points will inevitably end up falling back on tired sci-fi tropes—many of which were solidified during the Cold War era.