I need a replacement dungeon.

[Rogue Agent]

I have considered both Rappan Athuk and Caverns of Thracia, but the former seems too small and linear, while the latter seems to present some difficulties in the wake-delve-leave necessity of the game.

RA is less linear than it looks, particularly if you pick up RA: Reloaded. (And probably even moreso if you can wait for the new Pathfinder version coming down the pike.) Lots of side-levels and lots of routes that skip over levels.

The real difficulty with RA, however, is that it doesn't have a 1st level area. I'm guessing that's significant for the campaign style you're describing.

I really like Caverns of Thracia. Check this out.

But, again, not designed for 1st level play.

I think DCC #51 Castle Whiterock and World's Largest Dungeon are the only other megadungeon you're like to find designed for 3.5+. The latter is mediocre (and very, very linear); the former I haven't read.