The Be Invoked BD looks lush.
[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.
Animanachronism 
Like I said, make the bad guys more sympathetic by “making the good guys seem more like turds.” I’ll forgive you for lacking my eloquence, but I agree. I guess it’s the opposite method of leveling the playing field from what we usually see.
My anime viewing has slowed down immensely for the time being and I still haven’t finished the series, although I don’t live under a rock so I’m at least vaguely aware of how it ends.
It all seems, going back to Sheryl’s quote that I mentioned, very throw-up-your-hands fatalistic. “Eh, what’re you gonna do? People suck.” A lot is made of Anno’s mindset during the making of Evangelion, but I wonder about Tomino’s during this.
Where we differ is the ‘making the bad guys more sympathetic’ bit — I don’t think that’s what Ideon‘s trying to do, I think the point of making everyone unsympathetic is to make everyone unsympathetic. Which is not what you said.
It strikes me as fatalistic too, though there’s a note of hope in the way Be Invoked ends, which I won’t elaborate on as you haven’t seen it yet.
Xabungle, which Tomino directed after Ideon, is pretty goofy and upbeat. Assuming these shows’ plots are in some way records of his mental state — which is probably a shaky assumption — I doubt he spent those years entirely mired in depression. But I agree — I can’t help wondering along the same lines
A long time ago I’ve heard people summarize Tomino’s view as expressed in Ideon as something like “the adults are corrupt, the youth (which Tomino once had hopes for) are less corrupt but still unsalvageable, only the infants are innocent”.
I still haven’t watched Ideon, but I trust that person’s insight, and I can fully imagine how Tomino could come to such a conclusion.
In all honesty, I believe that too. Any sympathy is purely side-effect of the viewer’s adjusted perspective. I think it’s hard for most people to watch something where there’s literally no one worth rooting for. I have no problem for a while, but it does wear on you.
Shaky indeed, especially with so many other factors influencing an anime production. I’ll have to check Xabungle out when I’m finally done with this. I suppose you could also theorize that he worked out his misanthropy (or whatever it is) with Ideon, although like you said, there’s Zeta.
Net result is still the same, I need to finish Ideon. Any speculation on The Point (or anything else) is tough to make with an incomplete picture.