The Flyers are where they are because they have lost 22 games in regulation. Sens have lost 16, Isles have lost 17, Rags have lost 18. Shootouts and other arguments aside, you can't lose 22 regulation games in a 48 game season (with the NHL scoring system) and complain that you're not making the playoffs. Want to play in May? Stop getting beat.
The Flyers have been a level below NYI, NYR and Ottawa all season, even when the Senators had more injuries.
When Philly was mostly healthy the coach ran a press forecheck and encouraged the defensemen to pinch. This resulted in a ridiculous amount of turnovers and odd man rushes. Often there would be three Flyer forwards at the goal line, a pinching defensemen caught along the wall, and a 2-on-1 or 3-on-1 going back the other way.
For the first few weeks Bryz bailed the team out and put up good numbers, but after that whether due to lack of rest, lack of confidence, or just lack of skill, he was mediocre. When the injuries really started to bite the coach was forced to abandon that system and the Flyers started playing solid hockey. The team defense actually got better after Grossman, Coburn and Mezaros all suffered season ending injuries.