thats where there have to be limits and nerfing factors, it could be a back breaker, but it could also be a disaster/last ditch move.
lets say you have a smallish fleet, nothing too fancy, and youre out hitting neutrals for fun/exp/colonizing. your position is pretty secure and everything is going pretty well. all of a sudden your allys homeworld get attacked and he, for some reason, is weak as hell. you send your fleet in, and its juuuuust enough to beat them off. all structures are destroyed or the enemy is sending in reinforcements. you have like 10 ships remaining, basically holding the enemy at bay for your teammate while he rebuilds. well, because you have gotten yourself invovled over here, someone else is attacking you, and you are spread too thin. your ships arent going to make it back, and wouldnt make much of a difference anyways. you have a fleet back at home, but you need to pay attention to that, and not protecting your ally.
so you let him boss your guys around, maybe send them into an asterdoid with what hes built up so he can expand. because they are at half strength, youre really only there to be back up and bluff the enemy. which leaves his small fleet to go actually accomplish something. (say he could only get a colony ship out with your ships) if its just rebels, well even half strength ships can take them on while he colonize. maximum payoff, minimum investment. total last ditch effort to get yourself out of corner.
or because it lets the two of you sync up a bit better when phase jumping.
regardless i think it could a powerful ability. like domination for advent, but across the board and with a hit to DPS, or antmatter regen, or sheilds, accuracy, speed etc.
or allow them to be controlled as a "move to" but dont allow the other player to direct attack or use abilities. In any alliance battle group there are "supreme commanders" and then there are ally commanders. I reference NATO, there is a commander for all NATO forces in afghanistan, but each country has a CO, who takes cues and orders from NATO, but otherwise operates independently.
I think it would be a game changer, not a game ender.