[Their] awesome power, along with a dearth of insight into their real motivations, makes [them] a much less sympathetic villain. If anything, Ideon‘s means to a sympathetic villain is “make the good guys seem more like turds.”
Mike’s post is a very reasonable response to the first eighteen episodes. But I’d like to use it as a starting point, because it made me think: I’m not convinced that the show needs or wants us to sympathise with the Buff Clan. Instead, the verdict seems to be that we’re all bastards who deserve limited sympathy at best, and the only solution is to kill everyone.
That makes the famous kill-‘em-all ending sensible. It’s not even especially sad, once you think about it: yes, we’ve had enough of these too-human humans. Wipe the slate clean. Give them a chance to start over. Maybe the ending of Space Runaway Ideon is just—compare Zeta Gundam, in which the finale’s distribution of deaths and vegetative states feels unjust for, after all, the AEUG are good guys. They aren’t guilty for resisting tyranny, as horrible as their war was.
That said I can spare a little fellow-feeling for the Buff Clan, despite rather than because of anything Ideon itself does. Unpleasant as the Clan are, their situation—trapped on a rollercoaster of military necessities which they helped start—is not unfamiliar.