Well we can rule out it being a temporary throne room, as it is described in immense detail in the following article (also referenced by Max's answer): "Emperor's Throne Room", Wikia
Considering the following excerpt: Surrounding the throne room and its neighboring rooms was the abyss, an open shaft surrounding the turbolifts, which led directly to the Death Star's power core, 400 km (250 miles) below.
The receiving area, or inner sanctum, was separated by a retractable walkway.
The Receiving area was used for meetings with local system governors and/or the Emperor's advisors.
From this I would surmise that, being a Sith Emperor who rules the galaxy through fear, the Emperor intentionally constructed his throne room with an "abyss" in it in order to intimidate the governors and other people who would enter that room.
The fact that he could so easily be thrown into it served as even more of a "fuck you" to those people as it showed that he considered them to be of utterly no threat to him at all.
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Numerous areas throughout the Death Star consisted of vast air shafts.
These shafts helped circulate air, pressurise the battle station's habitable sections, and also channeled heat that expended from generators located within the shafts.
Imperial Death Star Owners Workshop Manual, p.82
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If I remember correctly, the Emperor's chamber was at the top of a tall spire on Death Star II.
The "pit" was simply the tower shaft.
See: http://starwars.wikia.com/wiki/Imperial_throne_room_(Death_Star_II)
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Echoing WayzGoose's excellent answer, the Emperor had the pit in his throne room because, well, it's very impressive.
And if you're the evil Emperor of a Empire consisting of several trillion inhabitants, it certainly helps if your visitors are suitable cowed before they've even gotten to speak to you.
THE EMPEROR has called for his servant, and Darth Vader has come to the Death Star’s immense throne room to receive his orders.
To approach the Emperor’s throne, visitors must cross a narrow bridge over a vast chasm.
If they dare peer over the edge they will see, a mile below, the terrible glow of the space station’s main reactor.
Then they must climb several sets of stairs placed there for no reason other than their own inconvenience.
There is no luxury in this throne room.
It is all girders and catwalks and strange machinery that hums, buzzes, and sometimes growls.
Even the throne is menacing, more like a chunk of black rock than a chair.
It doesn’t even have a cushion.
This whole throne room was designed for just one purpose: to intimidate.
Star Wars: Return of the Jedi - Beware the power of the Dark Side
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Intimidation.
Long, deadly drops cause unease in those coming before the emperor.
Especially when he has force powers to flick people off the edge.
It's the usual half-baked plan by an evil villain that backfires when he becomes a victim of it
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At the end of  Star Wars Episode 6: Return of the Jedi , Darth Vader threw the Emperor into a pit. Why was there a pit in the Emperor's VIP chamber on the Death Star?
Why was there a pit in the Emperor's chamber on Death Star?
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One might surmise that, as a Sith Emperor who rules the galaxy through fear, the Emperor intentionally constructed his throne room with an "abyss" in it in order to intimidate anyone who would enter that room.   The pit is very impressive hence why the Emperor has it in his throne room which he uses to communicate his orders.
The pit is very impressive hence why the Emperor has it in his throne room which he uses to communicate his orders.