After reading through this thread, I kinda got to thinking about something... The main problem seems to be that for the higher cost allies, the added difficulty of threat to Imperials is not worth the added ally.

According to the rules, a player is supposed to be 'in control' of the ally, correct? I think that's simply to keep the rules tight and is most likely redundant. HOWEVER, I think that may also be the secret to making the allies worth it. Here's my idea:

Whenever the player controlling the ally takes an activation, they may choose to immediately activate the ally so long as that ally is ready (not exhausted). If all heroes have been activated for the round but the ally has not been activated, the player controlling the ally has the opportunity to exhaust or activate the ally on it's own.

While it's a relatively small rules change, it can provide for a big benefit to rebels running allies as once per round you are able to get two activations in between the imperial player acting.

... or is that how it is currently intended to work and I've just read it wrong up to now?

Edit: read your post wrong.
Hmm, I dont really like this method, seems redundant. I believe the rules as are, are quite fine

I do not understand this. Perhaps it is a lack of sleep but I am just not getting it. An all can be activated and take its 2 actions whenever it is the rebels turn to activate a rebel figure.

He's saying that a Rebel ally that is brought along on a mission gets it's activation right after a hero does. Let's say Gideon goes, uses his two actions, then, instead of the Imperial getting a turn the Rebel ally gets to go. After that Rebel ally does two actions, then the Imperial activates a deployment and play continues like normal until the end of the round.

I don't know if this is any better or throws the balance off. The only allies I've ever seen the rebels get were Rebel Troopers. All they did well was die.