You could also try things like Yanfly's Plug-ins for Limited Skill Use:
http://yanfly.moe/2016/01/09/yep-56-limited-skill-uses/, and Equip Battle Skills:
http://yanfly.moe/2016/04/08/yep-90-equip-battle-skills-rpg-maker-mv/
As for elements. My primary backgrounds are writing and music, so I tend to take a layering approach to making games. I start simple, then add layers of complexity. I like elements because it's a fast way to add another layer to combat. Then I give each element at least one state it may inflict.
Or I tie it to something. Like Necromantic/Death magic stealing HP or MP, instead of normal damage.
Which is, of course, what most people do.
And that's where I tend to leave it. Guess I just don't consider them to be a vital, ahem... element, of game mechanics. I just think of them as types of damage that can be done.
One project I've got has 23 "elements". 4 basic forms of physical damage plus enchanted and armor piercing, 10 elements and magic types, and 7 racial types for Bane weapons. With occasional overlap, such as Necromantic. It's both a type of magic, and the racial type of undead.
One character in my last game has a spell called Torture that can inflict a DoT, and I briefly considered having a screaming SFX go off every time it proc'ed. But as amusing as I would find that, I figured most people would be a bit put off. Point being that you can give states and elements their own flavor with things other than mechanics.
Overall, my motto is "do what makes sense". With a healthy dose of the KISS principle. (Keep It Simple Stupid)
If something doesn't sit right with me for the setting I'm working in, I don't use it. And if I don't think it's adding something beyond complexity for the sake of complexity, I don't use it.
Like a Sci-Fi Setting. It really doesn't make sense that a flamethrower would do more damage to someone than a bullet, both are pretty effective. Albeit one tends to be messier.
But it does make sense that someone might have armor that the flamethrower will still hurt (heat is heat, and being on fire eats all the air), while a bullet might bounce off. On the other hand, someone might be in flame ******ant power armor that has an air supply... and then you'll need some sort of BFG.