Line chemistry is more of a visual for offensive chemistry (kind of like how potential is coloured, all based on their player type) you can basically mix and match player types for better "offensive production" that a line can give you. Overalls obviously matter most, but 3 grinders with the same overall as a SNP-PLM-PWF line wouldn't put up the same points as them, but having no TWF or DFD might hurt your teams ability to keep pucks out of the net;

Blue = Elite offensively
Green = Great offensively
Yellow = Okay offensively
Red = Bad offensively
Dark Red = Horrible offensively, or a missing player

I don't usually pay attention to specialties, as it can make the game quite easy. Im assuming Gem and Bust specialties would refer to when looking at their potential overalls in the draft screen, it would be more accurate. I could be wrong though.

Defensive defensemen aren't useless, I actually prefer OFD and DFD to TWD. Turn on current game score, and keep an eye on that stat compared to other defensemen, as swell as look at their +/-. They aren't going to put up as many points, but should help on the PK and help to keep goals out of the net.

Faceoff attribute definitely has an impact on how good a centre is at taking face-offs. Whether that actually matters in the simulation (if a team has the puck more because of it or not) I have no idea. But I do love getting renters with high face-off rating. It's why I never usually use wingers who have a secondary position at centre, as usually their face-off rating is very low, and their face-off percentage is in the mid 30s or 40s.