Etrian Odyssey-like Campaign; How do I properly make Mega Dungeons?

[Nishant]

The title says it all, really. I've never built a large scale dungeon, just smaller ones of one to three floors, and I can't confidently say they were 10/10. I've always been a fan of this game franchise, and thought it would sync well with either DnD or Pathfinder. Each 'Stratum' has a certain amount of floors, set to a certain theme, and are HUGE. there is generally 4-6 Strata, and I need to figure out how to set about it. One idea was the traditional 'Go Down/Go up' Then I figured while I could do that for a time, It may be more interesting to planes-hop throughout. I can figure out a motivation, and urgency would likely be rather soft until the latter half, when they learn of a certain truth, or are tasked to aid a major NPC. Right now I'm more concerned about transferring over design. (Another idea I had was a Mystery Dungeon feel, where certain floors or a certain Strata would be in perpetual flux.)

[noob]

You might try oblige if you like randomness.(a level generator for doom and many other video-games it makes awesome levels(with some 3D if you use 3D floors but if you want multi-layering just use the teleporters option and consider that a teleporter change your floor))
for huge dungeons try having something varied make a huge layout with open rooms or closed rooms and put many height variations of few all is a matter of choice and it depends a lot of the theme you wants also do not try too hard to do your dungeon around traps nobody thinks when doing architecture "I am going to make this trapped corridor everyone must go through" and also adventurers do not use corridors and will not go to "traps with a room around" it is rather the other way people build a building then some crazy bbe create traps at the weirdest places where there is no particular reason of putting a trap so that people get hit because they think there is no reason(unless nothing lives here).
Maybe you might think "do people live here" and then you take consciousness that
1: An useful corridor or room is not trapped if people are living here(Or they are crazy creatures) while rooms nobody goes to might have traps.
2: Put everything needed for your people to live then other rooms are Decorative/ Rooms for storage of stuff who is rarely useful/ everything else/ rooms for crazy enigma for acceding rooms that nobody wants to access except adventurers
3: Your creature needs appropriate supplies in food and water and so on(if you have any)
4: Huge buildings are for lodging groups of organized people not for random uncooperative monsters
5: Since people living here are organized they probably have a tactic like "when people are here we regroup and we wait them to trigger traps or to get to position where they are in disadvantage" so there will be only one giga encounter or something makes no logical sense.
One funny way of changing floor is shrinking stuff for entering a small from outside box where there is one layer of your dungeon where there is some dimensional magic(like a circle of teleport) making the act of destroying the box block the progression of the team.