Here are my couple of ideas.
I think the megadungeon should reflect the classic of the classic style dungeon setting. To my mind that means that the big bad guy inhabiting it is a powerful dragon capable of both speech, spell casting and the sort of mega villain leadership usually reserved for humanoid villains.
With that in mind I was thinking a ruined castle set on the shores of a sea or lake reached through a swamp or bog would be pretty cool. This would allow for some variation on using water in some fashion in some of the levels.
I thought the Dragondeeps might be a cool name for the dungeon itself and maybe the castle is known as Dragonwald Castle or something of that nature.
The ruined castle up topside and upper levels would be inhabited by minions in the service of the dragon and maybe there would be an evil dragon worshipping cult involved and dragon worshipping theme'd temples down below. Maybe the castle has a dark history of its own...maybe it used to belong to a line of evil nobles with some vampirism or undead stuff in their background so the crypts area might conceal an entire other faction of major bad guys that might accidently be released by the heroes on their way to down the big dragon bad guy in the lowest levels.
As a twist maybe the dragon turns out to be an ancient and extremely powerful dragon turtle. I dunno. Just tossing out ideas here. The dragon turtle could have been raiding and sinking ships for years litering the sea floor outside of the castle with broken hulls of ships. Maybe it has a way of getting inside that is impossible to enter without a specific magical key to keep the adventuring party from trying to get in through the back door.
Anyway. Just some very rough ideas.
Finished a side view map of the levels for the place, well for my idea anyway. Very rough obviously.