Consequences are great, but above all, be a fan of the player characters. They are the heroes and the avatars of your friends. The last thing you want to do is deliver a negative consequence that players interpret as punishment and that relies on your interpretation of past events (which could well differ from that of the players).
If they leave threads unpulled, things should change in their absence--but the changes shouldn't penalize them for making a rational choice based on limited information. The world should feel alive, but the opportunity cost of their choices shouldn't be catastrophe. After all, you let them steer. It's one thing to summon Tiamat if the GM says, "They'll summon Tiamat next Tuesday if you don't stop them," but Tiamat doesn't show up if they got distracted before learning about the ritual.