The thing is you can CC Ekko when he reaches at ~30% HP, that's when he's usually gonna ult. Most Ekko players are pretty predictable when it comes to this.
Zilean, however, no matter how well you time it; it's like a ticking bomb. The only thing you can do is either 1) bait it (and probably as well as some "important" spells) or 2) wait for Zilean ult duration to be over while that ally has already massacred your team. Maybe it's just because of the things I play, but Ekko (more like stupid ones specifically) IMO is more manageable because unlike Tryndamere, he can't mash R when CC'd, so a well timed CC spell at low enough health Ekko can just kill him off.
What OP should've brought up, though, is the insane amount of damage Ekko's ult does the moment he mashes that R button.
#R - Chronobreak
ACTIVE: After a short delay, Ekko blinks to his hologram's location, becoming untargetable for the duration, dealing magic damage to surrounding enemies on arrival and healing himself.
MAGIC DAMAGE: 200 / 350 / 500 (+ 130% AP)
SELF-HEAL: 100 / 150 / 200 (+ 20%「 (+ 6.6% per 100 AP) 」of damage taken in the past 4 seconds)
I don't know about you but that number alone is already insane.