I think there are many factors that contribute to this decision:
The time it takes to make a new map. The devs were probably already planning ST capital ships long before it was reveled there will be TRoS content coming. The devs took a lot of time to not only bring geonosis, but to also bring brand new capital ship interiors. With how every month there was only one planet added which were reused, i can assume felucia and ST ships were already in the works. Also the devs added 5 maps in OT supremacy in 1 update. Presumably trying to increase the quantity of maps.
There are a lot of people who don't like ship phases in supremacy because of how long it makes the matches, but they also want to play online and don't want to go to Instant Action just to play without ship phases. They probably designed OT supremacy for this specific demographic.
Also the fact that capital ship phases would all go to waste probably. Ship phases are only on multiplayer, and since they were preparing to add more single player content before the game ended, there was no need to add a ship phase when it probably won't even be used.
