Ok, from a technical viewpoint, I see it this way:
I favor a VOLUME based system for jump drive. As I understand the basic theory, and feel free to chime in if you think I'm wrong, jump drive works by creating a 'bubble' of jump space around the ship, and if that's even vaguely accurate than the ship's VOLUME is what matters, not it's mass. If the jump bubble encompasses the ship, it's based on volume and that's that.
Now, for ALL other movement I think MASS would matter, even if you have anti or contra gravity, mass matters and remains a constant. All AG or CG does is eliminate weight in a gravity well, but mass remains.
For example, if I could build a big hollow space station and take you all up into it, without some form of artificial gravity you could move a tone of steel, lead, whatever, if you could plant your feet against a wall and push on it because it has no weight, but you'd still have to expend effort to get it going and to stop or turn it because the mass is still there.
So while you could push around a cubic meter sized box of, say, lead, it would still b eeasier to push arounf a CM box of styrofoam even tho they have the same WEIGHT in 0g, because they still have radically different MASSES.
So, in cap, I say volume based movement for a jump drive, mass based movement for all other forms of propulsion.
As to gurps combat, there were some issues that were corrected in the 4e. Basically some of the big ones were:
You got a bonus to gun skills if you had a high IQ for some reason.
You had armor with a passive defense factor, which meant just by existing and sitting there, this armor made it possible for a shot to have no effect. The basic idea was that a well made piece of armor was curved and caused shots to defelect or skip off, but in practice it wasn't too realistic as putting on heavy armor lowered your dodge but improved you ability to avoid damage via the passive defense factor too much. They got rid of the passive defense in 4e.
Also, hit points were based on your health, but many people thought strength was a better thing to base HP on, and in 4e they base it on your strength.
Bullets in 3e did crushing damage, same as a mace, club, etc. Lots of people choked on that. Now they do piercing damage.
Lasers were way to potent in the gurps 3e with the autofire cumulative armor penetration rules, that's been changed.
Autofire in general was clunky and hard to handle in g3, in 4e it's been changed a lot and improved, the only thinbg now is that, thanks to the way autofire works, shotguns now have a recoil value of 1, same as a laser or other recoiless weapon. It's enough to choke on, but it's how they handle autofire and multiple projectiles like shotguns, the number of hiuts is based on how well you rolled versus the weapon's recoil. it's not too realistic to say a shotgun has a higher recoil than a .357, but when it comes to determining how many pellets of the blast hit it works out OK.
If you go to SJgames and look thru the gurps section you'll find an article on what they changed from 3e to 4e and why, it should answer a lot of your questions about combat in g3e and how it was improved in g4e. it's still not perfect, but it's impossible for a game system to be perfect.
On the plus side, gurps 3e had some great additional combat rules in the compendiums for hit locations, various damage types, etc.
I plan to run GT with 4e rules whenever possible. Also the GT starship mcombat system is pretty good, as are the ship deisgn rules when you add in the stuff from GT starships.
You could run GT with mostly 3e rules but make some changes to get the better parts of the 4e rules by using the 4e autofire rules, tho this mandates recalculating some of the weapon factors like recoil and bulk.