For one thing, the design would have to retain the overall appearance of the throne room at the top of the spire:

It would be interesting to see an actual ship with this as the "command tower", and then see the command tower detach, fly to the DS2 with the armada of TIEs and the like. The Spire rises out of the DS surface (be it the center of the laser dish or at one of the poles), whereupon the upper "jack" part docks with the top of the spire, giving us what we see in the original movie.

One could redesign the above structure to simply reduce the size of the side windows (to about 1/2 their current size) to account for it being a more substantial "palace" as well as command tower for an actual ship built personally for the emperor.

this could also incorporate Bingo's idea of the elevator shaft (instead of being directly over the DS reactor) having a window (either glass or force field) above and below the elevator shaft, thus when Vader throws him down, he bursts through the glass causing the wind and chaos (vacuum of space sucking out air and the like until shielding shuts the hole) or the Emperor still "explodes" as his body hits the force field glass, causing the energy wave going up the shaft as we originally see. Either way, if the idea is used, the bottom of the shaft would have to show the DS surface far below the window.

Also, the design above would account for multiple ramps coming from the elevator shaft, as they would go to different levels within the palace ship.

All images above are linked to their larger size originals.

Or you could just make it look like this: