Mutations implementation in Drox,could be difficult,due to variability of races of Drox agents.As i think it could be that Drox agent find an ancient ship of an unknown origin(could be few variation of ship look like),which has adjusted to the race of the new pilot(initial settings of the ship and improvements), and then as an option to obtain mutations of the ship to look for ancient technology(Dark Star One game have that,but in there player choose in what direction to upgrade/mutate) or as in Din's Legacy second line of experience for pumping mutations.
About Combat: auto aim was huge part in first Drox game,so if you want to make less auto aiming weapons,then maybe make aiming and firing on mouse and movement on arrows or WASD,but i still think that it could be an optional for autoaim.About movement can look StarCom Nexus and about movement and strafing look Star Valor and VoidExpanse.
About Graphics:in each new game the graphics are improved
compared to previous games,so its up to you
About Systems:make some planets have satelites(moons),that can give different bonuses to main planets,also maybe planets should move around suns(actualy not many devs do that,only Space Rangers 1&2 come in mind).