I agree, the ultimate does more damage than malzahar's suppression, and Ekko does it in AOE. I was shocked when they released the champion without a mana cost on this ability to boot (though that will be changing next patch). If it has a mana cost, I think it will be easier to justify the ability.....although I still wouldn't be against dropping the damage somewhat. I also think that the heal could take a nerf as well, but seeing as to how its one of the defining characteristics of the champion, I don't think it will get removed.
I don't necessarily think the ultimate is completely overpowered because where it is going to be is telegraphed visually, and if you are paying attention, you even know where it will be in 4 seconds. It isn't like a malphite ulti (or something like that), which has very little warning. With the kind of information you have about the ability, taking damage requires either bad position on your teams part, or very good positioning on the part of your opponents. If you force Ekko to use the ability defensively (he should be a priority target as an assassin) then the damage is irrelevant anyway. If your vision control is poor enough that you can't see ekko and he is allow to begin a fight with his ultimate............I don't really know what to tell you. There are many champions that punish pushing without vision and EVERY assassin falls into that category.
Strictly against melee champions; yea this ultimate is strong. I can only say see how it works after the mana cost is added? It should restrict him a little more. I just can't justify taking away the damage on an ability so heavily telegraphed. I don't know the range of the AOE, but that is something that perhaps could be looked at if they were to nerf it a second time. Also the ultimate has a pretty big cast time that takes the same amount of time regardless of the distance Ekko is traveling (I think). So if you are melee and against him, save your jump/gap opener for that crucial moment to avoid the damage. Remember, he is an assassin so against most melee champs (like fighters and bruisers) he should be having a tough time. If you take a melee, no CC, no gap opener champ against Ekko, you're in for a rough time; welcome to the wild world of counterpicks.
As for the passive W effect........while it is strong, I think it is fair due to the way his kit works. Without it, his damage would actually be pretty low. (DID HE ACTUALLY JUST SAY THAT??)
Let me explain. We have already covered the fact that his ultimate damage is hardly a part of his burst, as it takes either a mis-step or INCREDIBLE positioning to use it for damage, assuming he isn't forced to use it defensively. His passive, while high damage, requires 3 hits to proc and here we go with the argument. He needs his E to close distance on his target. (one proc) The problem is he is now VERY MUCH in range of anything his opponent wants to throw at him. Well, if his opponent is backing away, he MUST use Q to hit. If he hits with one part of the Q, his total damage is 290 +40% AP. If his Q hits both parts, he gets 630+ 170% AP.
This is actually some pretty crummy damage all things considered. This is his total "burst" assuming you are able to control his ultimate. Xerath non ultimate burst is 710 (for reference, I used sweet spot W damage; since I assumed everything from Ekko would hit, it seems only fair) + 210% AP. I could grab other mages and compare, but I take it you get my point; his damage is actually considerably lower. Thus I think his W is justified in having a passive that rewards him being up close next to his enemies; it would be too strong if his abilities proced it as well.
I actually have more beef with his shield strength than I do with the passive on the W.