The original megadungeon concept included fairly easy access points (at least from SOME levels

) and a location that was not too far away from a town so that beginning adventurers could have a chance to explore it and return to base if their skill and luck permitted.
For one of these to remain interesting for any length of time there needs to be interesting personalities doing interesting things beyond the monsters, traps, and treasures. In this respect a megadungeon is like any other adventure. It really doesn't matter what the plot happens to be, if there are no fascinating personalities doing cool stuff then the "plot" will be just as flat as the setting.
I prefer my megadungeons to have many connections to the world around it on many levels (both literally and figuratively

). All kinds of adventure ideas can lead from the surface, to the megadungeon, back out, and so forth. A fairly good sized body of rumors is a gread starting place for adventure seed fodder. Think about groups that might have a presence in the megadungeon, their agendas, and who might be allied with, or working against them on the surface.
I like to make sure when mapping out the levels, that a large portion of the map won't be actively inhabited. These areas provide a buffer between active factions, as do actual different levels. The "empty" areas can serve all kinds of uses. Wandering monsters can still be found there, some of which may be able to burrow creating new exits, entrances, and even connections to entirely new areas. Empty rooms provide a place to retreat from monsters or to set up ambushes for them.
When designing the inhabited portions, think about the inhabitants who will live there. If they are living then they will need food & water sources, and also some kind of sewage disposal. For groups that have been in an area for a very long time, think about what features they might have added or any remodeling that they might have done.
The megadungeon can still be as fun as ever but it needs LIFE! A static environment gets boring above or below ground.