Universe II - waaay over ambitious for the Apple IIe. Upgradable ships, trainable crews, in system flight/combat, boarding action tactics, trading/mining ... and a wee bit buggy.
There was a Jezzball-like game released into a CD in the late 90s or early 2000s that I cannot track down. Instead of using the mouse to create the walls, you used arrow Keys. I cannot find any trace of it even though I know I played it.