With that out of the way, get ready for some rambling...
Now, as we all know, there's little to no point in investing IP in more than a single weapon skill. That's good in a way, but it also feels (in my eyes, at least) a little like "min-maxing". After all, what's the "cost" of going for Kinetic instead of Energy? Sure, you can't salvage raids, but seriously, how often does an opportunity to do so really come up? So you "sacrifice" a decidedly minor option in order to get the same skill level with fewer IP.
On the other hand, if you explore derelicts, you'll often find them equipped with several different weapons - that's a nice touch for sure and certainly makes some sense logically (different kinds of weapons are supposedly better suited for different targets), but it lacks any connection to how WE know the world of CE works.
But how about this:
Certain ship types could be more vulnerable to a given weapon type (e.g. ships classified as "fighters" could be best fought with Kinetic weapons), translating into a SMALL damage bonus (similar to what targeting modules do). That would make equipping both Energy AND Kinetic weapons potentially useful, while not really penalizing anyone who doesn't do that. But "career combat pilots" might actually notice a (minor!) increase in their fighting power. It might also add diversity and tough choices (focus on one weapon type to get the strongest weapon or raise both to make use of this "vulnerability"), which would also be a good thing.
And then there are missiles. Sure, it's fun to sling the occasional missile at the enemy, but considering what the strong (read: actually useful) ones cost (in credits and invested IP) and how often they miss, that's not something anyone in his or her right mind will do regularly. Kinetic/Energy weapons are simply much more efficient.
So maybe something like this could work:
Instead of flinging as many missiles as one wants, one can only shoot up to 3 during any given combat (of course, the missiles would have to become decidedly more powerful with a much higher chance to hit). That would turn missiles from a fool's weapon into a kind of "emergency exit", possibly swinging a close fight in your favour.
Yes, quite a few enemies shoot missiles like there's no tomorrow, but that doesn't (necessarily) have to change - as far as I can see, apart from the limited number of shield recharges affecting both players and NPCs, there are differences between what WE and "they" can do anyway.
Last but not least, factions (combat factions specifically). As Coops already explained in another thread, GalFed/Confed are mainly "background noise" on purpose. While that's certainly nice from a player's point of view (less chance to screw things up) and would be almost impossible to change without seriously annoying a lot of people, it DOES rub me the wrong way, mainly because of the missed potential for more immersion.
One possible "solution" to this:
Instead of suddenly restricted access to something due to one's standing with the different factions gained before an assumed change, ENHANCED access to some additional toys might work. Similar to how access to most stuff in VP works (i.e. you can't enter certain shops without first gaining a certain standing), new/additional shops could offer something for those with the necessary rank/standing in a given combat faction, e.g. "GalFed Light Laser; Energy Skill 70; dmg 135-215; energy needed 300; rank needed: Petty Officer" available in addition to "Functioning GS-4 Beam Laser; Energy Skill 75; dmg 133-209; energy needed 335; lvl 12".
