For the Flotillas to have a decent game affect they still need to be close to the rest of the fleet. Whether that's their Squadrons or Capitals.
Relay. I've had fun throwing a Gozanti off away from the battlefield and relaying his 2 squadron command through a Shuttle. It still provides activation advantage. It's safe to activate at any point, since it's far from the battlefield, yet it's still commanding two squadrons a turn thanks to that Shuttle.
Then you're putting half of its utility on a 16pt Shuttle... Almost Doubling its Base cost...
And that half utility only lasts until the Shuttle dies.
Not saying its a bad idea... Just pointing out its not as cut-and-dry - you are paying a penalty, of sorts, for the ability to run and hide.