Bingo: how do you feel about the "giant imperial logo palace ship" thing? That would at least allow for a similarly shaped ship that would correspond with the existing top of the tower in JEDI.

Here are some more sketches:

The need to show Coruscant is completely redundant, as we do not need to see the Emperor leave, only arrive. One would need to replace the brief outside shot of the Emperor's shuttle, as well as change the Emperor's shuttle to an elevator IF THIS IS TO BE DONE. I can also see the Emperor's shuttle being colored red (or some similar slight change) or his shuttle being replaced with a unique ship to keep changes to a minimum as well.

The above storyboard is a suggestion of what could be done visually
(ala a "2001"ish appearance, with the sun behind, making the ship somewhat silhoutteted by the sun):

(1) palace ship arrives - lowers down as pylon lifts up to meet
(2) as palace ship lowers almost to docking, pylon docking claws seperate and spread out to attach to underbelly
(3) palace docks
(4) outer palace ring lifts off, leaving the center section still attached, which resembles the current tower top design (but with six branches as opposed to 4).