Poison is an element in FFII and VI-VIII but hasn't really regained it's status since then.

Holy gets quite a few options in early FFs but becomes more scarce in later entries with VII having one summon with the element and the actual spell being a plot device, in fact after VI, the spell doesn't get many options until FFIX and then you have to skip to X-2, XI, and XII.

Dark varies from game to game. It's featured in FFIV and then doesn't reappear until FFTactics, it shows up in four FF games as an actual element which are FFIX, XI, and XIV. It appears in more side games than it does in the main numbered entries.

Earth, Wind and Water vary but they generally get the most love in the 16-bit era and the MMOs with a few exceptions.

In terms of under-appreciated elements that have varied through the series or been fazed out, I miss enemies that have scripted counters for certain attacks. I mean VI-IX had them but either the game mechanics made them negligible or they simply lacked the bite of early installments.

I will also give a shout out to the Gambit system, which is still the best party A.I. set-up I've utilized in any game.