I'm thinking mostly of Season 1 and the screentime devoted to Wellick's corporate ambitions (his own hacker side story, paying bums to take out his aggression on them, the machinations of E Corp's CTO succession plan), but *especially* the season finale where Elliott is all disoriented in the wake of the hack and runs into Joanna on the street while he's looking for Tyrell. That scene in particular always stood out to me as something that would have to make more sense in retrospect, that we would eventually learn of some other connection between Elliott and the Wellicks that would explain the way that scene was scripted and shot.
The second season's withholding of Wellick, where his absence was such a glaringly important thread to resolve, didn't do any favors to those expectations either. I'd be more fine with how the characters were handled if the 'mystery' of what happened to Tyrell hadn't been dangled from the end of season 1 to, what, the middle of season 3, and then resolved with "well, he's just sort of a gullible loser, that's what happened to him."
But that said, I also haven't read any commentary by Esmail since the series ended, so I had no idea he had already responded to this. I'm not convinced it went off exactly as planned; maybe close, but it still ultimately feels like there was a piece missing, to me.