Having played extensively GalCiv2 (since Dec. 2005) and demos of SEIII and SEIV, I must say I miss the weapons/defenses system of SE. However, the reason I'm playing GalCiv2 and not SEV, is due to SE's brain dead AI. Once I got the weapon that bypasses normal shields in the SEIV demo, the game was over. I would build cruisers with this weapon and normal shields level V (in the demo I could not research beyond this point), while the AI continued to build cruisers with normal weapons and normal shields. A single cruiser of mine could take out a fleet of AI cruisers. I don't know if the AI was restricted from researching the more advanced shields in the demo but assuming it was it should have built cruisers with this same weapon to bypass my shields and armor which would have provided a limited defense.
In SE you have techs that increase your odds of hitting the enemy (combat sensors) and techs to decrease the odds the enemy will hit you (ECM); plus the odds of hitting a small fighter are lower than hitting a dreadnought but the dreadnought can fire on multiple fighters at the same time. Shields and armor absorb hits from normal weapons before the ship takes damage. There are special advanced shields and armor to counter the special weapons that skip normal shields or armor.
My hope for GalCiv3 is a complex weapons/defenses system like SE while maintaining the quality if the AI (i.e., the AI should design optimal ships based on the strengths/weaknesses of enemy ships). Many have asked for tactical combat in GalCiv. In SEIV the AI was poor at tactical combat so unless victory (without any damage to my ships) was assured, I took manual control which increased micro-management. I would prefer to keep it out so as to keep the playing field more even between the human and AI players.
In short, I would like the more robust combat system (minus tactical combat) of SE added in a future GalCiv3 but not if it cripples the AI (because it can't cope with the added complexity).