Unresolved things
So that General took some serum and became pretty much the Hulk, but he just leaps away never to be seen again.
Amazo teleports some light years away to avoid Grundy from absorbing his energy, and never returns
Amazo's too powerful to ever be resolved, and is a storybreaker whenever he shows up.
I might have liked to see another episode involving General Eiling, but after his realizations in Patriot Act there's not much character left to develop there unless he were to start becoming less fanatically anti-superhuman and pro-'Merica. Unlikely, given his attitude.
Maybe a situation where he and Superman were forced into a temporary team-up where they traded discussions on the issue in-between action scenes, but then Patriot Act was late in the final season anyway.
I'd assume Eiling eventually got Superman's attention and they had a confrontation - maybe physical, maybe only philosophical - and I'd hope Superman was able to bring him around. It's unlikely as you said, Eiling was too hard-line (which is counter-productive with almost anything) and probably took his hatred of metahumans to the grave.