For roughly a week now in trunk, tweaks have in place to allow Zot to use more than the one standard level layout previously necessary for all levels with a primary vault; it's now subject to one of several layouts (cf.
evilmike's suggestion).
I've poked a few players that have played through this "slightly revamped Zot", and it seems to me that their perception of the place hasn't changed very much. Granted, a week isn't very much time to gather a significant amount of feedback, but I tend to trust the opinion of those I've queried about this; thus, I'd like to try to stoke the flames of this discussion some more.
I don't think that trying to torque the established feel of the game *too* much (such as blocking upstairs until one has the Orb) is the right approach - Zot should be a place that requires all the skills the player / character has honed throughout the rest of the game, and throwing completely unexpected changes at them isn't the right way to go about doing that. It's an established challenge at earlier points in the game for a character to get into, and back out of, heavily guarded areas - runes and the Orb itself, particularly, illustrate this best, as do some branch entrances (in particular, Zot entrances) - so having, say, the down stairs guarded heavily in the manner I originally suggested seems to me as though it would be an appropriate challenge.
If the vaults that are necessary for this are sufficiently well designed, it would provide enough of an additional challenge to make the branch the interesting and climactic place it deserves to be, regardless of the character's play style.