There was one particular plot point that I really thought would be used again.
It came up once in season 4, as a way to explain how Brenner kept Henry under control. It was capable of completely suppressing his powers. Quite a feat, really, considering those powers came from an interdimensional being.
If memory serves, Henry even pockets it after El removes it for him. But it never comes up again.
It's especially odd considering that we learn about it in the same season El is trying to restore her powers. The only explanation that we're ever given for this is that she had a mental block and had to go through her suppressed memories and come to terms with them. It had nothing to do with the fact that her powers vanished after she was attacked by the season 3 monster and had a piece of it in her leg. A piece that we later see reintegrate with the rest of the monster.
That could have been a good way to explain El somehow being implanted with Henry's Soteria, or something like it that he devised after keeping the version taken from his own body.
It also could have been a way to explain Will's neck tingles. He could feel the hive mind, but not interact with it, because the lab inserted a Soteria into his neck after season 2 "just in case." His ability to tap into the hive mind in season 5 could then have been explained by having a scene where it's somehow removed beforehand.
But, no, that also never happened. El's powers left and returned simply because of a conveniently timed mental block, and Will's extremely inconsistent connection to the hive mind, even after he was purged of shadow particles, was never explained at all.
Soteria, which was given a (seemingly meaningful) name and everything, was nothing more than a contrived plot element to explain Henry being under Brenner's thumb for so long. Why did they put effort into pointless things and so little effort into what mattered?