One idea I had while playing BOTF and Supremacy is Fleet Control of your Allies. What I would love to see in Supremacy is you the player being able to take command of your allies fleets so you can coordinate attacks against your enemy.

Maybe set something up in the Diplomacy Screen where you can select a option : Take Command Of Allied Fleets. Depending on your relations with that ally (100 = accepted, 20 = rejected) you will gain control over all their fleets. The AI Will still be able to have control over their fleets just not the ones you gave orders to.

This system currently works in Hearts of Iron 2 by Paradox Interactive. Its a great system. I would love to see it implemented in Star Trek Supremacy. Especially when you have a enemy that has 3x more ships than you and you need your allies resources.

*IF you need to get a copy of Hearts of Iron 2 let me know.

A standard diplo action of attack race X in Y turns would do. Taking control of AIs' fleets is most likely exploitative.