Honestly, I'm all for adding some new aliens. You could even integrate aliens into Star Control 1 without actually changing the plot much at all.
There are three categories into which these aliens might seem to fall.
1.) Un-uplifted races. These species would wind up being, basically, either planet-bound or system bound. They wouldn't have the spacial infrastructure to participate in the Ur-Quan war in a meaningful way, but could still be a source of resources, information, and even technology to the interested player. The Slylandro are a good example of this in the Star Control 2 universe - if they had been encountered by someone other than, say, the Melnorme. It stands to reason that there may be many of these races out there, and events such as the Yehat's uplifting of the Shofixti are the exception, rather than the rule.
2.) Low-population / imported races. Most of the races in Star Control 1 are very, very local. The Ur-Quan didn't bring a bunch of races from outside the map, and even neglected to utilize the Thraddash, despite their existence as battle-thralls. Perhaps the Ur-Quan could have races that they brought from much more distant sectors, in order to utilize their tactical or logistical advantages? The biggest rule, however, is that the Ur-Quan don't want new colonies outside the borders that they set for their battle-thralls, so they would be used sparingly.
Perhaps, then, we could even see some misbehaving, and attempting to create a covert colony, which you might blackmail / recruit later?
3.) Neutral races. Star Control 1 focused entirely on the conflict between the Ur-Quan Hierarchy and the Alliance of Free Stars. Without changing the makeup of either side, there is plenty of room for races that are space-faring, but don't either want to join up with the galactic conquerors, or place their ships on the line in opposition. The Melnorme qualify here - by being an entirely shipbound race, and hanging out in regions that are inhospitable enough most Ur-Quan wouldn't think to look there, even if they had the technology to overcome the massive interference, they avoided both sides. The Arilou nearly qualified, but weren't willing to let humanity fight alone.
I could very easily envision a race of space-pirates, who attack the supply lines of both sides during the conflict. Perhaps, using some technology to disguise themselves as members of the enemy - perhaps their ships even have the ability to swap their primary weapon with the weapon of ships they've salvaged, outside of battle... or their primary weapon is very bland, but they have a tertiary ability to fire a limited number of shots, as above. Their ships would be cobbled together, and their mannerisms would be as piratical as possible.
Their homeworld, if they even have one, could be in an asteroid field so dense, you'd have to be an Arilou to get to it, or have navigational sensors well beyond what most ships are capable of.
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The two biggest things I'm concerned with don't involve the inclusion of new races. They are, first and foremost, that the character and appeal of the original Star Control races is preserved. This makes some of the races, like the Utwig and the Supox, a bit more difficult to include. How would they enter the conflict? Would they be relocated? Would they have been pressed into service as battle thralls? Would the Utwig still have lost their Ultron?
What about the Orz? The Orz entered the galaxy by wiping out an entire human sub-species. How would you keep the same balance of cute, babbly fish and eldritch terror?
The second thing I'm concerned with is game balance. As I said before, Star Control's combat system is essentially a fighting game, and those are incredibly notorious to balance. The larger the roster, the more difficult balancing the characters while maintaining truly unique character mechanics and styles becomes. Since this is a reboot, it stands to reason that the player will have more than 2-button capabilities, which means that the races that do exist will need to be retooled somewhat in their operations... I'd be cautious about attempting to add many combatants right off the bat.
