Energy
In the original Star Control there was a single energy bar for both systems. If this SC intends to keep ship at 2 systems each, possibly 3 on one or two, then it could use separate energy bars for each individual weapon or device. I would strongly recommend this. With such simple ship designs a single energy bar for both systems is very restricting. It eliminates a lot of potential weapon/system designs from consideration all by itself, greatly complicates the design of some ships, and certain weapons/devices either can't work together are will work badly with another system interfering with their energy usage.
For example, take my 1v1 dueling "dream ship" that I mentioned in another thread. It's weapon must be fully charged to fire. While this could still work with a single energy bar, it means that dropping a mine temporarily disarms the main weapon (until the energy if full again). This makes the ship significantly less capable, and is annoying from the players perspective. With separate energy bars using the mine has no effect on the main weapon, the systems don't interfere with each other.
It's more natural to the player that they be able to use a thing they have not used yet/recently, and not have that thing not function because they have been using a different thing. If you have guns and a shield, in such a simple game, you expect the shield to function when you try and use it if you haven't used it for a while. You have your two capabilities, and often want to combine them. Separate energy bars ensure that you can.
But the most important reason for this is the simple design of the ships. A single energy bar eliminates a LOT of variety in the design of weapons and devices, much much more is possible in ship design if each weapon and device can have it's own special rules for how it works such as things that only work when fully charged. It also allows fine control over the rate of usage of each system. It just enables a lot more variety in the design of the ships considering how simple those designs are.