Hello,
Okay, I've been a super long time fan and still play the original. Star Control 2 story line and ship fighting is what made the game to actually be so AWESOME.
SC3 story line was bland, boring and well as predictable. If you want the Reboot story to be a success stick with the story line or start with the beginning story line pre-star control two. Well that story is pretty much already written.
Story Lines:
1.) I would make story line very extensive or meaning multiple chains or ways to go.
2.) Variant Endings or several endings depending on the path you take.
3.) Precursor findings and story line hints of what may of happened to them.
4.) Have all of the races that were destroyed by the UrQuan. The Taalo, Burvfixes, Dynari and many more.
5.) Unzervault is Found and the precursor ship is built towards the end.
6.) The Hierarchy defeats the alliance or does it? That ends of this one can constitute an altered future of the original SC2.
7.) DLC Content or additional story lines.
Game mechanics and physics:
1.) The fleet size in SC2 was rather small. An increase fleet sizes if your flying around in a special ship.
2.) Different Ship Variants. The only thing that lacked in SC2 in my opinion was ship classes. For example; Battleships(UrQuan Battlecrusiser that can lauch fighters), Cruisers, Destroyers and fighters(UrQuan Fighters).
3.) I don't think the ships all need tons of weapons, but must have special abilities like the yehat shielding, Illwarth Cloaking and etc.
4.) 3D QuasiSpace, Hyperspace and Regular Space like in Sins of a Solar Empire. In this realm you have one ship you command and sub ships in your fleet. You can either attack another fleet with all, one ship or a series of ships and all the way down to actually piloting the ship. IF possible.
Star Trek Online style of system travel is some what cool.
5.) I would keep the star bases and add abilities to colonize. I am sure before the war or before humans entered the war they colonized the entire solar system of sole and outlying systems.
6.) The ability to setup solar system defenses and star bases that can defend themselves and be stocked with with weapons.
7.) Just like SC2 the fleet circles move meaning the entire fleet is on the move. The map should still show the radius of the fleets reach and power.
8.) Special Precursor weapons that could be found that were not in SC2. The ones from SC2 well those races still contain those devices and well we can't get to those due to technology or lander limitations or because those races have control and there is no word of it.
9.) If tech is mentioned maybe have the player actually search multple solar systems like hint the specific region that might consist of 5-6 solar systems in a specific set. The hints in 2 made you think, the hints in SC3 where way to easy!
10. ) Research and resources still a must or Melnorme Traders still offer unique tech for data samples.
Game Must Haves:
1.) Multi-player ship fighting or if possible
2.) Multi-player race wars. You head up a specific race and fight another.
3.) Multi-player Story line play if possible.
Or make Star Control Online game where the story starts from SC1 and continues as seasons to get to the SC2 story line and then on forward. Kind of like Star Trek Online and etc this would be a cool or later idea.
Just some of my ideas!