Megadungeons need neutrals. There shoudl be a faction the players can interact with that isn't there solely to be defeated or isn't out solely to screw-over the PC's but isn't there as a first-aid kit or rescue squad. Megadungeons need Neutrals.
In most dungeon adventures we have Irredeemable Foes, Selfish Foes, Foils,Dumb Beasts, Feeding Horrors,Victims, Allies and Competitors. Not a lot of real variation in how Irredeemable foes are dealt with they are there to be defeated. Selfish foes are there to be thwarted or destroyed, the goal is still defeat at the hands of the PCs and most people are going to treat them the same as irredeemable foes (roll initiative and attack) sometimes a selfish foe can be bought off or tricked to help for a while but this is really just delaying the inevitable destruction at the PC's hands. Foils are a trickier manner, they usually pose a puzzle that must be solved if they can't be treated like an irredeemable foe, once the puzzle is solve they are usually of no remaining use to DM or PCs. After the foils we find ourselves with dumb beasts, they are there to eat you if you are too slow and stray into your territory but they aren't really bad guys; players will still treat them like irredeemable foes 99% of the time but onc eina while a player with a special ability will exploit and control a dumb beast (often reducing it to a piece of equipment in execution). Feeding Horrors aren't worth interacting with and are darned icky and want to eat the PCs, the PCs will generally avoid them like crazy or destroy them no greater interaction to be expected unless someone figures out how to get the feeding horror to eat someone else in the megadungeon. Next we have victims which are usually walk treasure and will be treated as cannon fodder if they aren't walking treasure. There is the rare and unlikely allies which players will lean on and exploit to no end and honestly if they are useful and capable why aren't they beating the PCs at their own game. Competitors will sometimes be mistaken for Allies, victims or Foils but when the players discover their true nature they will seldom last longer then a kobold holding a gp. That leaves us with neutrals.
The players have to be able to tell they are dealing with neutrals and not foes or competitors or you aren't going to get very diverse play out of the situation. The neutrals have to stand apart from the foes in some obvious fashion but should also be a fair bit different from allies/competitors.
One way to get the neutrals to stand out is to make them a breed apart. Throw in some obvious non-PCs that aren't a variation of an established monster race either. Moss Elves, Root Gnomes, Pebble Dwarves are cheap and easy way to go but one could go a step further and have Mole-men or mice people or something decidedly different from what the players are usually expecting in the first place. Many players are goign to hack first but yuo have a chance of a conversation coming up and then an opportunity for the players to discover they are dealing with neutrals.
The neutrals can of course serve as foes/foils/allies/competitors but they are really in the megadungeon to do their own thing. It's up to the players to define how they are going to relate to the PCs. Sure that might mean a hack-fest. But neutrals provide a faction to be bribed, hired, stolen from that just might encourage a wider range of role playign options beyond...fireball wand or stab them with a sword?
Get some neutrals into those megadungeons.