My biggest gripe with the current system is that weapons, which take up ship hardpoints, require that you sacrifice a crew/upgrade slot. That's silly. It's a hardpoint, a point on the outside of the ship specifically designed with all the room required for the weapon and its proper functioning. It shouldn't take up any room required for upgrades or crew. At this point the hardpoints are just upgrade/crew slots that also have the ability to hold weapons and that just seems silly considering we're already so restricted on the number of upgrades/crew we have. That means even the ships that are currently out which have 6 module/crew slots will be even further restricted if you chose not to buy a ship with any "fixed equipment."
As it stands there's no real point in differentiating crew/upgrade/weapon hardpoint slots. They all just take up the same slot. If this is the route that's wanted then there's absolutely zero point in buying a ship that doesn't come with weapons and then trying to arm it, it's better to just have a ship that comes with "fixed equipment" weapons, because they take up no slots, so you can use the rest of the space for the people/upgrades you want.
I also agree with the OP, however. The module/crew slot thing, I'm not a fan of that, either, yet I kind of get it. Modules like that would, theoretically, take up areas inside the ship and the ship only has so much internal space so it's either a crew room or a module room. Makes me think a bit of the game FTL where some ships start out with empty rooms but you can buy certain "modules," for example a stealth module, and suddenly that room will have a console in it and be dedicated to the new module.
Having to balance energy during battle makes sense and makes things different to ground combat and, in such, a bit more interesting; even having to choose between automated upgrades and number of crew is reasonable, I don't really like it, but it's certainly reasonable. Having to essentially take up a whole room in order to accommodate a weapon, which already has a specially designed hardpoint for it, doesn't make any sense to me. If nothing else that is the thing I'd very much like to see changed, just allow hardpoints to be hardpoints and once you're out, that's it, no more weapons. If that means that ships with "fixed equipment" weapons have more weapons and upgrades/crew than others, then so be it. It'd even be reasonable to reduce the amount of hardpoints by, say, half, as long as they no longer take up upgrade/crew slots.
That's my two cents, anyway. I found the combat fun, I think it's going in a good direction, and, so far, I'm happy over all as I have no other issues with the ships currently on offer, the combat, or any other system currently integrated in terms of space-stuff.