Let's not also forget that the Rebel leader woman even says "...and the Emperor himself will be there."

Soooo, space palace or not, Palps has to be there, since that is their motivation to going all-out... you know, other than ANOTHER Death Star being built and all.

Also keep in mind that the whole thing was a trap set up by Palpatine and he wanted a front row seat... this is not something he wants to Tivo and watch on his crappy 20" hologram projector.

You know, maybe one could create a scene where Palpatine has a bag of popcorn and a soda, enjoying the mayhem...

On a more serious note, maybe the Emperor's ship could look like this:

with the "palace" fitting within the black area in the middle (when the ship arrives, the center piece comes out and attaches to the spire).

And just to be different, it could fly vertically (ie this would not be a top view, but a front view)

This would give some further significance to the Imperial symbol, as it would literally represent the symbol of the Emperor and his control of all six (?) corners of the galaxy (with the Grand Moffs signified as the outer spokes on the wheel, extending his power).

Also (Bingo), this could make up for the second Death Star idea. Rather than having 2 Death Stars, maybe the above Emperor ship could have a similar (but smaller version) of the Death Star laser array set up in the six points on the outer circle (that the entire outer circle is the weapon). While the rebels find out about the new Death Star, it could be explained that no one knows anything about this ship, so when it arrives everyone is completely shocked (including the imperial soldiers and officers, who never knew about it either).

It could be taken out by the Executor by Piett, who then drives it and the Executor down into the Death Star, opening a hole in the Death Star's shields (at least the ones that the "fully operational battlestation would have"), so when the rebels destroy the back-up on Endor, not only are all shield considerations taken care of, but the Executor/Emp ship crater would provide the opening for said attack force to go down into.