A possible reason I have read on why the A380 is inherently heavy compared to, say, the 747ADV is the fact that it needs the floor between the two levels which stretches throughout the length of the fuselage.
I'm not so sure as to that. For one thing, the A380 makes extensive use of new materials like the GLARE (aluminum/fiberglass laminate) in many places to reduce weight, and it was designed using digital CAD software which improves structural efficency. The major weight gains came from two things IMO-
1. Like AvObserver said, the A380-800 was designed with a stretch A380-900 in mind, seating 700+, and thus has a much stonger wing and centerbox design than would be necessary for just a 500 passenger aircraft.
2. Singapore Airlines requested (read demanded) larger engines and a tweaked wing profile to reduce noise, allowing 24-hour flights without restriction into LHR
. These engines and noise reducing features added several tons in unexpected weight, which compounded the already heavy (though planned) weight of the A388.
Either way, a shrunk A340-700 would need to go on a serious diet if it were to go up against the much lighter 747-Adv.