Ekko is unreal unbalanced currently. at lvl 6 with 0 kills / equal farm ... I have 70 MR in items (Negatron Cloak / Spectre's Cowl ) - he can roll into me and drop my health by 70%. No other AP character that I know of can do this. I don't know why MR doesnt impact Ekko's kit - but it really needs to be looked into on Riot's end.
Probably got sheen. Its some pretty spooky damage early in the game. (his E applies Sheen)
his e does AA damage also, plus sheen, ludens, statik, deadmans, and any on-hit effects
I get the impression you're not giving us the full story
what were his items?
mr really screws him over since his base damage early on is, to be quite frank. really low outside of passive early on.
if you had 70 mr by that point in the game then he probably had sheen which makes his e deal a good mix of physical and magic damage
if ekko has something say... 
then you have 55 mr, now lets take into fact he probably ran pen runes, (so what's what, Eleven?) now you have 44. extra mr with 250 extra hp.
so with that bit of extra mr he could do about half if not more hp with two parts of his q + e for passive thunderlords sheen bonus, which you deserve to be hit by if you let him get both stacks of his passive from q on you.
if you want a trick to help with him as veigar ekko when he blinks will always appear infront of you try aiming aiming your cage with this bit of knowledge. Treat him as a ranged champion. Yes, he's melee, but his e is exceptionally powerful to get into the face of people trying to get frisky and get into aa range to farm safely, putting them in harms way of being combo'd. when he uses his q to push, FIGHT HIM. He just used a huge chunk of his damage on the minion wave to push it to roam, fight him as he only has aa's and his e to fight you, get a quick trade in this time as early on before he buys cdr it has a decent enough cd to warrant a quick trade.
Just my two cents from an Ekko main.
ekko is insanely broken tbh. his ult and his passive damage need nerfs. and his ult in general is retarded as fuck.
Ekko's biggest problem is his ult. For a champ that can one-shot targets, stun multiple targets while giving him a great damage shield, dash away to escape or engage, and slow targets while damaging them in the process twice, his ult is overkill. It allows him to play like zed. One shot the carry, and get out unharmed. Yes, fizz can do the same, but fizz cannot get his health and mana back.Akali too, but she needs a nerf just as bad as ekko. His ult has a short cooldown considering the utility, damage, and flat out game-changing potential. He has no counter play once he gets his ult, his kit gives him THE most outplay potential. Either rework his ult or nerf his kit.
"I suck with an overpowered champ, that might be because the enemy champ is more overpowered than mine"
[slayer-jinx-catface]
