First of all congrats to Obsidian for their amazingly successful Kickstarter campaign. As a huge fan of your older games, I am really looking forward to Project Eternity! Anyway, I just had an idea concerning the Endless Paths and thought I might share it for others to discuss or at least tell me it's crap.
Considering that this dungeon is going to be HUGE, I think it would be great to make it a place the party returns over and over. I am not talking about locked doors that can only be opened with special quest keys, though. What I would prefer is a more oragnic approach: Simply make the lower levels so dangerous that the heroes need to go out to gain more experience before they can return to the Paths with any hopes of survival. Tie the dungeon into the world, but separate it from the main story line (side quests might lead from the latter to the Paths now and then), but I would like to see this dungeon as kind of an optional challenge that is really tough to take on - and provides rewards that are worth it, maybe something completely unique like a spell that cannot be learned anywhere else, an exotic NPC party member of a race normally unavailable or a pet that can be found only in the paths (and must be defeated before it joins the party).
Overall I am very confident that you guys at Obsidian will create something awesome with this dungeon, whether or not you like these thoughts of mine.