I didn't really think you would go down to 3rd person view - stuff like that would probably beyond most AAA companies. But it is good to know that you are planning to make the Emperor's ship stand out in some manner. On that, are you planning on allowing customisation of the Emperor's ship itself? Any examples?
I really do like the idea that if a battle is too far away, then you can't control the battle itself. As an added level of depth, have you thought of adding limited 'personalities' to even the ships under the Emperor's control? As in a military commander deciding that your order is idiotic/suicidal and ignoring it? It might make for interesting gameplay, confronting the player with the options of whether to allow some level of independent thought (and thus higher chance of winning battles) at the risk of increasing dissension or beat your subjects into slavery (lobotomise, etc) but mean that they are all but useless without your command.
I'm also curious as to the level of politics your planning on implementing - will there be royal court back-stabbing and feuds to deal with? World dissenting from the Emperor's rule? Assassination attempts? On that note - does the player start out as the Emperor, or as a noble climbing the ranks?
Finally, what level of technology will exist within the game? Will it have the Fading Suns/Foundation aesthetic with a collapsing empire where most don't understand the tech that they rely on, or is the empire still in the expansion stage of development? Will it have something like the church from Fading Suns declaring certain tech to be 'black' or 'immoral'?
Sorry for the long post, by the way - I hope it hasn't put you off

.