A central command ship is all about versatility. The mother ship from Homeworld and the Pride of Higara from HW2 as well as the kith-somtaw ships all survived their adventures because they were incredibly versatile. They had storage facilities, hanger bays, construction capabilities, FTL, command centers, Intel facilities, and ect as well as the ability to further modify themselves as the situation progressed.
QIS built an orbital ring system that was later named Helix. In a nutshell it was a self replicating star base capable of a multitude of tasks. The only reason it is still lasting is because of its ability to harvest resources independently so it can grow and modify itself
ISDF mother ships (battlezone2) are not easily modified but can gather their own resources and thus operate for extensive periods of time away from earth.
So to boil it down to three things, versatility, resource gathering, manufacturing ability.
Also, if you want help designing the ship or want me to try making a 3d model tell me.