From Frogboy's previous postings, the new Star Control is going in the direction of a series reboot; with emphasis on the "First Contact" era, when the Chenjesu (as representatives of the Alliance Of Free Stars) first made contact with humanity.
Based on established cannon, the Chenjesu & Mmrnmhrm formed the administrative/economic core of the Alliance, with the Yehat filling combat roles, the Shofixti serving as scouts, and Earthlings filling an exploratory role. The Syreen never had formal membership in the Alliance; they were caught between a Mycon & a hard place when the Ur-Quan showed up, and chose to fight with the Alliance. The Arilou's role in the Alliance organization was never truly explained in Star Control I or II. According to cannon they show up without warning shortly after humanity joins the Alliance, and request membership; but the role of the species was never clearly defined, and leaves tons of room for interpretation and/or adaptation within a new continuity.
With this in mind, I would like to think that, at the time the Chenjesu contacted Earthlings, the Alliance already has an organizational structure, so there would already be an existing "Fleet" with established commanders. Cannon suggests there was a level of mutual respect between the Yehat & Earthlings due to both species having achieved significant advancement (interstellar travel) without being "uplifted" in the way that the Yehat influenced the Shofixti. Based on the martial nature of the Yehat, it would make sense for a strong Yehat influence in the upper echelons of the Star Control fleet command structure. It was also noted (I think by the Melnorme in SCII) that the Mmrnmhrm had several minor border skirmishes with the Ilwrath, prior to the Ilwrath becoming battle thralls, which would indicate some level of defense-mindedness on the part of the Mmrnmhrm. Given the loose affiliation of the Syreen, I wouldn't be surprised to see a bit of disdain towards their species from the full-member species; nor would I expect to see Syreen officers in positions of significant authority within the Star Control chain of command. If playing as an Earthling (an assumption I believe we've all been making), I could well imagine some of the senior officers/officials of senior Alliance members taking umbrage with the "new guy" coming on the scene and making waves within the organization.
If this is going to be the prelude to the Ur-Quan conflict, a cold war if you will, between the Alliance and Hierarchy, than strategy elements would be great. While some races should, for story purposes, be dedicated members of the Alliance and/or Hierarchy, it would be great to see new/expanded races choose their alignment based on player decisions. A great example lies in a potential change to Star Control II history: The Fate of The Zog-Fot-Pik.
What if, for whatever reason, the player had chosen to ignore the distress signals from the Zog-Fot-Pik in SCII? We know the answer: the species was history. However, what if the player HAD decided to aid the beleaguered frungy lovers, but put it off for a time in favor of higher priorities, and upon arrival was faced with the newest, albeit most-reluctant addition to the Hierarchy of Battle Thralls? Granted, it would likely have been a slave shield, but stranger things have happened...just ask a Spathi.
The SCI method of building bases and/or outposts also has merit. Since fuel is a finite resource, having a place to hang your hat while the ship is refueled makes sense, and provides for an interesting place to pick up story/side-quest options. If you want to recruit a new species to the Alliance, but said species is afraid to commit due to a lack of Alliance resources in the area, and a homeworld in close proximity to Battle Thralls, what could be more comforting (or threatening, if we're talking about "convincing" a member of the Hierarchy to switch sides) than putting down an outpost/starbase/battle-station in their backyard? However, with resources being finite, players should have to choose carefully where and how to assign them. Reinforcing the "core" species sphere's of influence/homeworlds may keep the major power centers relatively insulated from conflict, but it would come at the expense of fringe elements (allies who's sphere is out-of-the-way) who may reach a tipping point where the benefits of Alliance membership are outweighed by having to constantly bear the brunt of enemy forces. However, spreading the fleet across the entire alliance may leave the heart of the Alliance vulnerable. Again; player choice is paramount.
One of the neat things introduced by the good folks at "we sold millions of units by ripping off Star Control" was the idea of a persistent universe. Performing tasks via an app-store mobile game, or in non-story multi-player in Mass Effect 3 had an effect on the single-player story; it affected the effectiveness of the player's single-player gains, which had a direct effect on the ending.