His system revolves around the idea of puck possession. Cycle the puck back to the D in all zones instead of forcing it to the center of the ice and risking a turnover. Just watch how often they go D to D in their own zone before attempting a breakout pass. They almost always try to get their D-man the puck behind the net, and would prefer the D skate the puck out of the zone (possession) instead of attempting a long pass. This requires mobile defensemen who can skate and handle the puck. Notice there's at least one of those types of defensemen on each pairing... Myers, Ehrhoff and Sekera have the puck carrying duties. Leopold is also pretty good at it, but he's not as fleet of foot. It seems teams have figured this out, watch how hard they forecheck Myers, Ehrhoff and Sekera.... and force turnovers.
In the defensive zone, the forwards collapse inward toward the goalie instead of running around chasing the puck. This helps to keep pucks to the outside and force long distance shots. Shot blocking plays a key role. This is a sound defensive philosophy, however you need to two things: 1) a goalie with excellent vision and 2) players willing to block shots. Miller's strength is his positioning and quick feet. IMO, vision is his weakness. He struggles to pickup pucks through traffic. He lets in a lot of long range floaters from the point, that any beer league goalie would easily stop without the traffic in front of him. Watch other goalies on long point shots, they'll battle to find the puck, up on their toes, hunched over, bending in all directions to find the puck. Miller doesn't do this too well, he relies too much on his positioning with the idea that the puck will just hit him if he's in the right spot.
In the offensive zone, they try really hard to get the puck back to the D for a one timer. Teams have picked up on this, defensively their wingers often play very very high in the zone to take away the pass back to the D. This puts added pressure on the forwards to beat their man one-on-one or thread a pass deep in the zone. Buffalo just doesn't have those types of players. In fact, they have quite the opposite, small fast skaters who are better in space than battling in tight in the corners. I've noticed this during the past 3 losses... lots of turnovers deep in the offensive zone because they're getting muscled off the puck and can't get it back to the D.
It's not a flawed system, when it's clicking, it works quite well. However, I see a failure on Lindy's part to adapt his system over the past 4-5 years. He needs to change it up, add more wrinkles through out the game to adapt to what other teams are doing. Quite frankly, he's getting out coached on a regular basis.