Remember the Barry that stood up to the big guy when he went to visit his dad?? Yeah, I miss that guy....
Now I'm not saying that Zack's Barry was a completely different character, it wasn't, but Joss made him into a "too much" part; via Ezra's performance, Barry obviously deals with anxiety (which is amplified byt this particular pickle they find themselves into) but he deals with that by trying to overcompensate with confidence, not the overbearing kind, mind you, but it's a simple "won't let you see me break down" type of body language (which you can see in his first encounter with Bruce, the security footage from BvS, the SS cameo, the aforementioned prison scene, etc); despite his fear, inexperience and hesitation, his heroic nature shines through; my favorite single moment, the complete look of determination and lack of hesitation when he starts his run to face Superman in the memorial site.
Again, I'm not saying it ruined the character, but I feel that Joss looked at that and went "quirkier!! QUIRKIER!!!!" and instead of understanding the
why and the emotional mechanisms of the character (as constructed by Zack/Ezra/Terrio) he went for the more superficial (and honestly, easy to get for the masses) approach to the character but sadly ended up making him, again, "too much".
While all of this is mostly assumption based on observation, I believe it to be the result of a lack of unified vision in the final product; hopefully that problem won't be present in future appearances by the character.