Given my love for Ekko, as evidenced by my changed summoner name, I may be viewed as biased, but here are my thoughts on the changes that could be made to nerf him while still keeping him viable.
Q: The return trip is what you have to watch out for, as the ratio between outgoing and incoming is 3:4, and that's not taking into account the +60% AP it gets compared to the +20% AP for the first half. Lower the damage on the second part, either through reducing the base or the AP scaling, and I think that's enough.
W: As it's tough to land, I'm okay with it having a little extra power. My issue with it is the shield. When you're turret diving, or being turret dived, you can become a tank for 2 seconds. A shield of 330 at max level, not factoring in the AP scaling? This is, in my opinion, the part of his kit that needs nerfed most.
E: This I'm okay with leaving mostly as is. However, I wouldn't be completely against increasing the CD.
R: Going based off his lore, and the cinematic, this ability should be more about the 4 second "reset" he gets, not the "nuke" (as people have called it) he gets upon returning. 500 at max level, plus 130% AP scaling!? I rarely even go for kills with it, instead choosing it to do things such as steal dragon with my E then back out of the 1v3, ult back to lane, get HP back in a sticky situation, etc. Yet I still find myself getting kills with it whether I intend to or not.
TL;DR: If you're going to nerf-hammer anything, target his W's shield and the damage on his ult. The rest only really needs minor tweaks, in my opinion. Just please, please, please don't do to him what you've done to so many champions recently that you've nerfed, or even tried to buff/rework, and change him so much that he's rendered virtually useless except in the hands of the truly skilled. That's all I ask.