There's nothing wrong with Flaherty. He's missed a lot of time due to covid related reasons, but his velocity is intact, swinging strikes are identical, and his K/BB ratio is similar if only slightly worse than it was last year. His xFIP (incoming Boxy rant) and by extension xFIP- is actually even slightly better than it was last year. He was always unlikely to come close to repeating his second half performance from last season which had significant batted ball luck, unless he actually got better which is certainly possible given his age and talent level, but unlikely in a season like this one.
I don't think Wainwright has actually been their best pitcher (a .228 BABIP in a small sample size will make a lot of pitchers look good) though certainly the most reliable, and I agree he's fun to watch. In his prime he was an ace in a team that consistently went deep into the playoffs.