Things I have noticed (sorry if they have already been mentioned, I am too tired at this point to read all the posts). They don’t make the game bad, they just go against physics. It's ok though b/c you can’t really make a game that is both fun and respects every law of physics. Starcraft is a fine example...Marines that are 1/8th the size of a battle cruiser that is supposed to be full of people?
-Fighters that fly through space as if they are WW2 warbirds. It’s fine for the sake of making the game fun, but if the game was to implement a more realistic physics model, the fighters should fly like they do in the TV show Babylon 5.
-Ships not being able to leave the gravity well of a planet.
-Capital ships getting stuck in space when they are trying to move b/c they are surrounded by tons of frigates and no in space collisions.
-An inability to shoot down incoming missiles or use some sort of ECM to jam them.
-Missiles having a limited range in space when their initial inertia should allow them to continue to move through space even after their fuel supply have run out.
-Ships being able to take direct hits from weapons with no apparent damage.
-An inability to target specific subsystems on a ships
-Wave weapons…seriously, what are these? Made up weapons to make the game more fun so it’s not entirely missiles and beam weapons.
-Phase missiles missing their target and then making a 180 degree turn instantly to go back and hit the target.
-Laser bolts in space that change course.
-Ships taking damage from laser bolts and mass driver weaponry that has not actually hit the target, but hit behind it.
Among other things...Anyone could make a huge list, but its about making the game fun and playable so that's what is most important.