I feel as though I've seen and responded to this same spiel three or four times already in past threads.
Your disappointment seems to sit mostly on the fact that evil wasn't vanquished and society didn't become a peaceful utopia because some teenagers discovered the secret of the magical mecha. Fair enough, you don't like the conclusion, but that doesn't mean there wasn't one.
One could ask "what war would you call a success", but instead maybe it's more convincing to contradict you directly and point out that Simulacra's entire defense consisted of the Simoun because they were religiously attatched to them. This was successful to a point due to their sheer ridiculous power, but stagnating in this way leads to getting torn apart by industrious enemies. You might call this a component of those "themes" that people like to talk about. So yeah, they lost. That's the point.
Other than what's been said, I thought the part with Dominura served as a slight lampooning of the anime technology mindfuck trope -- trying to figure out something advanced to an arbitrary degree beyond your understanding so that it has seemingly magical powers will only hurt your head. The helical motors are empty and undissectable. That's what messed her up.
Aer and Neviril created their own heaven or nirvana, separate from time and space. Religious transcendence. I could write one of those hilarious internet anime analysis term papers if I wasn't behind on actual work