That's the Odyssey from Stargate of I'm not mistaken. It does have a nice design, though if we include it, it needs to be yellow

Anyway, the purpose of a mobile command ship is for commander to be able to command his forces in any skirmish that's out of reach of the main base, the command center or whatever. Maybe after TS, GDI found a better way for a commander to command his forces in a skirmish, without needing to be nearby. For instance, GDI could have a network of satellites around the planet (which -since they are a network- are obviously connected to eachother), via which an oversight of the battlefield is given to the commander and radio signals are transferred. That way the commander can even be instructing units on the other side of the planet without needing to be there.