Restrictions - Though the Racial Restrictions are there to balance out the game and include flavor and context for Galaxy Prime, one may choose to eliminate them entirely and make all races equal across the board.
Points - If you feel the players dont have enough starting Skills, Languages or Mutations, you may wish to give them 100 points towards that purchase instead of 50.
Credits - For those that want to give the players a jump-start on their finances (and possibly put them closer to purchasing a ship) one may double the initial starting credits.
Defects - Some may feel that the Defects are unduly harsh. If so, they may be ignored.
Disorders - Some may feel that the Disorders are unduly harsh. If so, they may be ignored.
Weight - For those that do not wish to deal with the constant calculation of Carrying Capacity, feel free to let the PCs carry whatever they want.
Cyber - On top of the normal cost of Cyberware, the price for "installing" it could be included.
Dodging - If you feel uncomfortable letting people dodge lasers and such, you may want to eliminate the Dodging rule. Or if the characters die too quickly and easily, allow them to use an action to attempt another Defense roll.
Criticals - These can be very harsh and getting rid of Critical Hits and Misses may help the game to go smoother.
Luck - While it can still be used for other checks (against poison, etc.) it does not have to be used to tweak one's rolls. Disallow Luck rolls if it unbalances the game too much.
Maneuvers - Using too many Maneuvers may drag out space combat unnecessarily. Get rid of these for a quicker fight.
Power - For those that dont want to deal with the inner workings of a ship, feel free to ignore the rules on Power Transfer.
Pain Check - It adds a bit of reality to personal combat but is not necessary and may be ignored if desired.
Gravity Difference - Tied in to Carrying Capacity and Combat, this rule may be eliminated if it causes too many re-calculations.