Seeing to many ekkos today and reminded me why this champion even exists. Hes terrible in lane and you can obliterate him with ease mid game rolls around and he just mashes r to save his life ever 2 milliseconds. Can we have a change to his r to make it as long as shens? Saves should be a sparing ultimate not something you just mash every teamfight with basically 0 cd.
Get good scrub.
His kit can be pretty hard to deal with if you haven't memorized it. He does have many windows of opportunity for you to destroy him. Good luck on the rift friend!
Sounds like you're wasting your cc (should be saved for when he is at half health or below so he cannot ult), using your cc far too early, have no grievous wounds (noticeably hurts his healing), or are not paying attention to where his ult is. If you're beating him in late there is absolutely no reason you shouldn't be able to kill him in teamfights. He needs items just like any other champ to do damage, and if he gets his items he WILL do damage regardless of how well you did in lane. Of course that's applicable to any champion in the game, more so for champs who scale decently. Also Ekko is not the only assassin/mage with an invulnerability frame ultimate that can save him as well as mobility 
(his being on his E which is spammable). There is a hefty list of champions that are more problematic to deal with before Ekko is worth a thread. Sorry.
