What this game needs (among other things) is a mod for weapons that would make them clearly different and distinct.
Under Engineering should be two new lines, one for Information Systems and one for Power Sources. All weapons should have very low range, accuracy and strength, which can only be improved by researching IS (range and accuracy) and PS (strength) respectively. IS could give (modest) bonuses to economy and PS to manufacturing. Not sure if IS and PS should be represented by actual systems on a ship but overall I think not - not enough displacement available now.
PS research 'could' also improve shield strength and movement speed, and IS 'could' improve point defense, but I think this might be unbalancing. Perhaps if all shield and point defense units were reduced in original strength?
Weapons should be modded to make them uniquely valuable; I will use Beam weapons as an example, but the same concepts could be applied to missiles and mass-drivers:
Lasers should be low-power, short range and very fast-firing. Positron Beams should do moderate damage but be inaccurate and slower-firing. Plasma Beams should be very high damage, short ranged and very slow-firing. Phasers would be more like lasers: longer-ranged, accurate, do moderate damage and be faster-firing.
Making real differences between weapons allows the player to select the system(s) he thinks will best benefit him, not just push blindly up the tech tree. You might be better off (for example) in the short-run to research IS and PS to improve your existing laser-equipped ships, lengthening their usable life span while you research Positron beams build new ships (or amass a fortune for upgrading).
One last change: each defense type should include 33% of its primary value for the other two types (so for example a shield unit should provide 8 shield, 3 armor and 3 point defense points).