Challenge #1: IS Star Control Star Control without the Spathi?
Spathis are an old favourite. Having the Spathis around would be tantamount to getting home, putting some well-worn-but-comfortable slipper and enjoy life.
I don't want confortable, in real life. I want to be challenged. The world is my playground. I want to know what lies beyond the ridge, over the chasm, at the bottom of a pit, in a natural cave or in an abandoned building. Slippers are nice, but I'll trade them any day for boots to travel and discover in. I'll sometimes long for my Spathi slippers but the better the reboot game, the fewer and father in-between those moments are going to be.
Challenge #2: What IS Star Control?
In its strictest sense, Star Control is the Earthling's space division. In effect, if you don't have the Earthlings in the game, you can't have Star Control in the game. This having been said, Star Control is, also, a philosophy, a way to view the wars: you control stars / star systems, with the ultimate goal of overpowering your opponent. SC1 managed this solely through war, while SC2 managed this through diplomacy (mainly) and war (somewhat).
What SC2 introduced beautifully and became (I believe) the most interesting aspect of the game, is exploration. SC1 had some of it, but it was rather limited. SC2 allowed you to find new alien races, precursor artifacts, dead civilizations, lore, new dimensions, etc. This is what struck the imagination of most.
From my understanding of these (and other) forums, what people are looking for is the feeling of novelty, of discovery. The moment when you realize that the Mael-Num and the Melnorme are related (if not the same species). The moment when you hear through the Melnorme that a civilization was destroyed by the Druuge to deflect the ire of the Kzer-za.
That is what constitutes the Star Control experience. Without any link whatsoever between the new game and the prior universe, however, it will be "a new space exploration/rpg/action game by an old name". You need to get some lore (at least) in the new game, so there is a feeling of connectedness. Mechanics, space exploration and a name are not enough to integrate the reboot with the old games. If you could at least get the precursors in, see a rainbow world being created and interact with, say, the Taalo (even if briefly), then you've established continuity.
Challenge #3: Defining some core values
Determination to awe the players
Ambition and boldness
Commitment to revive the franchise
If you miss your mark on the fourth one, you'll effectively kill the franchise forever. It took 25 years and a beyond-dedicated fanbase to give SC another life. If it is an half-assed attempt at life, the fans will kill the game and will prefer to cherish fond memories than to have mixed feelings towards the current incarnation.
Challenge #4: Satisfying the super fans
You can't please everybody, but you can please most. In Wing Commander: Privateer, you could make it as bounty hunter, as a pirate or as a trader. If you could make it somehow possible, in SCR (Star Control Reboot) to allow players to be more combat-oriented, more exploration-driven or trading-oriented (think of StarFlight II for trading), you will effectively cast a very wide net, that will allow you to mitigate whatever impact your "Beyond-hardcore-I'm-stuck-25-years-ago-and-it-was-better-that-way-with-no-internet-and-top-down-combat-and-the-Ur-Quan-are-there-and-I-want-the-Arilou-and-the-Spathi-and-(whatever SC2 was)" fans will have on the community.
I'm not saying not to cater to them. But don't cater too much to them. You're not doing a remake of SC2.
The precursors located rainbow worlds to shape an arrow that pointed towards a different region of space altogether. You are doing that. Sadly, the races of the first 2 games are not going to be there, but let's embark on a new journey.
Oh, and I just want to mention a way to have Humans that wouldn't be Earthlings in the new game: The Humans of Earth stem from the crew of a lost Colony ship of the Original Human Race. The crash was disastrous and they went back to the stone age, eventually losing everything they had: history, technology, etc.
Sorry for the long post, but I like to explain myself fully.