Really great topic. Let me add my 2.000.000 cent coin purse and lets have a chat.
I’ve addressed this topic before, but in a different way:
Basically my take is, to have distinct mechanics, each with their own merrits. If every skill has a good appeal, because of their distinct functionality, there is already enough reason to use it / see it get used. I don’t think the goal is for everyone to like every skill, but they should be viable and somewhat unique in functionality. A nuke skill should not ALSO provide huge stagger AND have a low windup AND have long range. Pretty difficult to make other skills shine then… 
Split the functionality more into categories, add more categories, buff/tweak them enough to make them attractive vs pure DPS and provide each in a more varied fashion. We can go a bit into more detail if you’d like, but if they would focus on that (and that may simply require some number tweaking), I’m sure we’d have a lot more varied playstyles and rune variety.
@Chemile0n Just a sidenote, as you were talking about it a lot; Maybe my PoV can help: Imo you SHOULD be able to use every Rune effectively against every enemy (when it comes to the dmg type). Otherwise there is always one dmg type better than everything else and overshadows the rest (think about Echoknight - If he’s weak to something - guess what you will be using against him and are more likely to build around). Also you are restricting the players playstyle by forcing them to use different elements to do their damage → LESS flexible Rune slots → LESS actual variety not more. And LESS fun: Oh i want to play a plague build, yay! Oh the Echoknight is resistant to Plague… Guess I play something else… Or go play another game entirely, which does not screw me over. Sorry for the exxageration, but I hope this helps 