I believe a more accurate way of putting it would have been "Barry was only depicted that way in two series which featured him very prominently, and which were also essentially his only appearances in the last 23 years".
Barry Allen "died" in 1985.
In the decades that followed, he got rare and brief appearances, usually pure flashback (and some of those were written by Waid, who used the JLA Year One version).
JLA: Year One was a major series featuring him as one of the main characters.
Flash and Green Lantern: Brave & the Bold? He was the co-star. He was the "Flash" in the book's title.
There is a distinct difference between ignoring those appearances and ignoring Tigra's use in Civil War (in which she appeared very briefly and barely got any dialog). It's closer to choosing to ignore, say, how she was written in the Tigra miniseries that came out not all that long before Civil War.
Of course, you're still left with the question "Should Johns really take his characterization from only two instances in Barry's history?"
I'd argue that Waid's characterization of Barry has much more in common with the pre-Crisis Barry than Johns does. Johns even goes so far as to shoehorn tragedy into Barry's past.
It's true, things definitely got dark around the time that Reverse Flash "killed" Iris. If Johns wanted to write Barry as being "dark" in the present and use that as a justification, I'd disagree with his decision, but it would be a very different matter. But that's not what Johns is doing. Johns is channeling Hunter Zolomon and retconning Barry's past, to say that Barry was always a serious and tragic figure.
That's Johns deciding he doesn't really like Barry's characterization from any instances in Barry's history.