You're leaving out a very important factor..
PLAYER DEVELOPMENT
The Flyers have not only failed to develop the existing skills of these players, they outright ruined/are ruining many of them.
This is a red herring. Their prospects haven't under performed relative to their draft position (other than the flops, and talent was the issue, or health).
Frost hasn't been stifled, he's struggling the way a #27 pick normally struggles at the beginning of his career.
TK is playing fine, especially for a #24 pick.
Sanheim is a solid 2nd pair D-man, good value at #17
Farabee is more than good enough for #14.
The one player who has faltered is Provorov, and in hindsight he may have been an overdraft based on his early physical development, i.e., he is the same player he was as a rookie (excusing this season, which I believe is probably an anomaly).
The point about two way players has some merit after the 1st rd, you're always looking at players with flaws, Flyers tended to put size and physicality over skill, at least until recently, so you get Ginning, Ratcliffe, Laberge, Allison, etc. in the 2nd rd. Bunnaman, Dove-McFalls, Vorobyev, Twarynski, St Ivany et al in the 3rd and 4th rounds. Fletcher at least went for York, Brink, Andrae, Tuomaala, Millman the last few years.