Power lines, and other ENGINEERING features
First off, let me state I love the game and have been following it since before it came out. Secondly, let me state that I almost never play it. Why? The reason why is because I'll open up the game (go through the slogging process of adding all the mods to make it less EMPTY), and build a ship. It isn't very hard or time consuming to build a ship except for grinding the resources since there really aren't any engineering REQUIREMENTS to building a ship in the first place. Locomotion? Strap some ions/hydrogens/atmospherics on the hull anywhere you want and, as long as they're pointed the right way, it will move. Power? Slap stuff onto the grid and it is powered. I'd like to list out a few things I think should be added to improve the engineering aspect of the game (problems to overcome in each and every design, which adds DEPTH) and why I think they should be added.
With power lines, you can no longer just slap stuff anywhere on your ship and call it spaceworthy- now you will have to route power through your ship like a real adult, and making a bad ship means damage can damage those power lines, crippling your ship.
Heat, and coolant
Because engines and nuclear reactors DO actually get hot- guns too. It should be simple enough to copy the conveyor code but instead of items it contains coolant. Then to make coolant from oxygen. The compressor would both function to make coolant and repressurize it like in a real AC system. One would also need fragile radiator strips that must be protected but can vent lots of heat in batches. Additionally, copper pipes could be wired into an outside-edge block to make it constantly vent off small amounts of heat. (All of this is infrared radiation). Disposable heat sink projectors are not necessary but would be neat for combat. (Imagine emergency venting your coolant into space to prevent meltdown? This would be a very cool scenario, but then you've boned your ship for the next few minutes while it repressurizes.)
There is a mod that already does heat but while a great step in the right direction, merely requires that you slap blocks on the hull in order to vent heat.
Just like power lines into ion engines or atmo thrusters would be nice, the powerful hydrogen thrusters could use dedicated fuel lines (again, copying conveyor code but not making them connect) instead of just hooking it into conveyor network and calling it a day. I do not know about you, but I do not like my computer boards covered in starship fuel.
With these three things added, different ships will diversify the way they are built. Commercial non-combat ships will likely see a main bus of all 4 tubes going through the middle of the ship and branching where needed, but military ships will have to provide redundant systems to be less vulnerable, and feature more passive heat venting or disposable heatsinks.
Crappy tier parts
What if, and bear with me for a second here, what if there were a tier of parts below the standard one that are super easy to make (like being able to make an assembler with bare hands, thus enabling 0 infrastructure survival start), but break down over time when they are used - requiring regular maintenance to keep them working. This too would influence ship design as you would not place any components hidden away where you cannot physically access them to repair.
Damaged components damage blocks
Right now we have green radiation leak effects from damaged reactors and flame ones from other things, but what if these actually dealt damage? Radiation leaks could make machines malfunction and damage players but not blocks, and fires would damage players slightly while raising the temperature around them and damaging blocks, especially non-armor blocks. This would open the way for adding blocks that are damage control, like foam spewers or nanobots that repair things (there are mods for the latter); all this would add depth. You could vent parts of your ship to put out fires, or removing fallout laden gases so you can go in and fix the issue.
Last, and probably least, long range combat options.
I know you can make personally steered torpedoes, write a script to steer torpedoes, download someone else's script to steer torpedoes, and download mods so your torpedo doesn't look like a blocky turd, but that's dodging the main point. Simply expanding the max range of the sensor block or adding a seeker block that can feed tracking data into a script could go a long way into making space combat where you don't have to build a new ship every time you fight due to the mutual damage. (Yes yes, auto repair or shield mods but that's a flame war in a can of worms I am not opening)
That is all I have for now, but there are probably lots of other things too that would expand the DEPTH of the game that is currently lacking - though there is plenty of room for it. I know Marek has said in his blog that he plans more things like this, turning it from a sandbox into a game, so I am just pitching some nice ideas out into the ballpark, so to speak. :)