I've been playing around with the game and doing some casual ship modding over the past 3 or so days and have so far really enjoyed the combat. Since my time with the combat I've come away wondering about a possible alternative path for shields.
Right now (correct me if I've misinterpreted a game mechanic), shields are used exclusively to protect against explosive damage. Raising a shield to protect against energy or kinetic damage essentially overloads your flux resulting in a dead ship for a short period of time - something that is never pleasant to have, least of all during a fire fight.
And I cannot help but notice, that shields are currently only usable against the only damage that can already be defended against (discounting heavy shells). Flak cannons and vulcan turrets amongst other things, can take down torpedoes, missiles and presumably any other future high-explosive delivery system.
So why the overlap? The role shields play in combat could be expanded to make combat more varied. One possible idea would be to increase the amount of flux delivered to shielded targets by energy weapons, and making kinetic damage completely negligible against shields resulting in both damage types (and their weapons systems) having a more defined role in combat. Kinetic damage, in order to have a distinctive use, could then be given an armor piercing quality allowing it to partially (or fully?) bypass armor and directly damage the hull.
I'd love to hear what you think about these suggestions - it could very well be that you've already laid out more involved plans for the various weapons and defenses in which case most this post is probably irrelevant