On the topic of dead ends - I hope there will be several ways to complete the main quest and you'll have to work hard to screw this up.
To go back to an earlier example; the killing of the rangers, and thus the breaking of chain of command and death of main-quest giver. (Granted main quests comes from ranger HQ). Just give us a key to a locker somewhere, let the leaders diary be in the locker, and let us continue on our own. Maybe we have to go a detour, maybe killing the leaders are a shortcut towards our goal.
Basically, just give us several ways to complete the main storyline, and let them all be viable. And note, by different ways to complete the main storyline I don't mean "Well, you have to get item X from room Z, you can either blast your way there or sneak in". They should be completely different, like for example, following the chain of command and receive quests from your superior ranger, or kill said ranger and carry on by yourself. However, some kind of conclusion to the main story should always be reachable one way or another.