Imagine having more interaction with space :

Ion storms, Solar Flares, Time Dialation, Black Holes and Asteorid Fields affecting navigation and speed..

Now suppose you wanted to jump to a certain planet but to do so you have to construct some sort of stabilizer to do so.. ^^

Imagine being able to construct stabilizers on any jump point to increase the speed of a jump..

Imagine having to use impulse drives to get to certain resources neighboring a planet but you have to go through certain anomolies to get there..

Imaginee being able to create a pocket universe with phase jumps to hide your fleet and hit and run planets, save your damaged ships,

Discover ancient listening outpost in the spaces between phase space that you can acquire and have vision of some planets\

Imagine an ever expanding universe...

Discov3r time travel to change the outcome of battle for only a few seconds.

More organic worlds

Weather systems

Discover space-living

Ships

Imagine engine exhaust flaps moving, Guns spining to charge up, flaps opening that act as exhausts, or ships reshaping and transforming certain parts to allow phase jumps.. and abilities to activate (e.g the Engines of the USS voyager in Star Trek Voyager)

Discover space dweling creatures  captur3 them and use them to aid your enomy or military..

Construct actual planet killers..

Construct Assimilator ships that take over starbases

Dynamic damage effect, explosions, movements.. ships that tilt and turn like fighter jets when turning...

Discover.. after burners on light frigates..

Discover wreakage of weird ships destroyed in ancient battles..

Races

Discover race characters and personalities.. develop personal relationships with these characters.. their stories, there victories, their sorrows, their sadness and there war.

to be continued....