You wrote a lot so I'll just point out a few things I agree or disagree with you about.

I agree that the Necro Prime's (shooting additional bone spears) rarely gets put to use.
But if it was removed from the Prime I believe it would be smart to add it to a different item.

The Dragonslayer Jewels magic resist modifier may seem a bit useless but not many items add magic resist as it is.
And even with a ton of magic resist, surviving against magic attacks is nearly impossible or at least in my experience.
I'm not sure if more magic resist items should be added or if the enemies with magic attacks should have lowered damage.

Treads of Valusia should definitely gain something to make them more interesting, I agree they aren't used much at all.

All other Items I have no comment on at the moment, I don't play enough of all the characters to know what's what.