I think the spires are a nice idea poorly implemented. I think a full rework is in order, but that doesn't mean spires shouldn't be a part of it. They should just be a more logical, useful, and reliable element of his kit. For example, what if he got some other passive, and his spires were worked into an active ability in place of his W.
Q - Unchanged. Spammable AoE damage is fine. Maybe work in some % max health damage when near spires.
W - Places a spire, like a ward but with a tiny vision radius. They can be destroyed and are visible but still hide in brush, like Control Wards. Being near a spire builds up a shield on Skarner. This shield provides a speed boost equivalent to how much it has stacked up. This builds up decently fast out-of-combat when near a spire, and gives you an initial amount of stacks the moment you drop one (even in combat). When outside of spire range, you slowly lose that shield/speed buff over time. It isn't lost as fast as it's gained when out-of-combat near a spire, but still encourages him to "take territory" like the Crystal Scar map (may it rest in peace) and his current spire system, but gives him control over where that system is placed.
E - Similarly fires a crystal in a line that marks enemies, but applies a weak slow to them. Basic attacks amplify the strength of this slow. However, if a crystal spire is nearby, they charge up a beam over the target's location and attempt to fire a Lux-style beam at that spot, but narrower and weaker, obviously, with a shorter range. This beam can be dodged, but if Skarner clings to you and slows you enough, dodging is hard, and the beam does okay damage and turns the slow into a stun.
R - Base damage is lower, but each nearby spire also tethers a beam onto the target dealing damage over time as long as they are within range of that spire. One nearby spire would mean pretty much the same damage as before, but more spires nearby means more damage than it has now, maybe scaling down any subsequent spire damage after the first.
I think this would be a great way to keep the same idea without it being so arbitrary, and without feeling punished for not hiding in some set area of the map that serves little purpose like lane objectives do. He could take his spire mechanic to lanes with him, and have a sort of mini-game still without being bound to the jungle and giving away his position all the time. Giving each move an interaction with his spires and letting him place them himself would go a long way toward making this character fun and useful again without damaging his theme.
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