I somewhat agree with you, OP. It really depends on what champion you're playing and the person you're playing against. Thus far I've faced two Ekkos in top lane as Shen and the first one was....well....I don't wanna say brain-dead because that's overkill and mean, but it felt like it. Constantly using abilities to waveclear, often out of mana, if he was LUCKY his Q would smack me on it's way out. I don't think it ever hit me on the way back in. He ended up doing pretty badly since I was easily able to taunt him before he could use his W or simply walk out of where his W was setting up. The second Ekko I've seen was better in that he could land skillshots, and he gave me problems, but ultimately his mobility was just an annoyance more than anything. He still ended up negative and had to roam to other lanes to try and get kills. (at which point I pressed R and the potential for those kills vanished.)
IF he catches you, he hurts. Yes. No doubt about that. But I think you can say that about any assassin. IF the enemy team happens to help him, you have a high chance of being dead by the time the fight is over. But those are both 'if' scenarios. They could go in your favor just as much as they could go in the enemy's favor.
Just like with anything else or any other champion: be aware. Two of his skills are skillshots and can be avoided (you could call his ult a third, but it's a bit difficult to keep track of it sometimes.) That's 2/3rds of his damage down the tubes. He's strong, but he's not THAT strong.