I'm totally on board with revamping the power systems! Almost any other minigame I can think of would better then the current minigame of running a mess of spaghetti noodle power lines through a ship, and then cramming a giant capacitor tank inside. Anything that makes the game more interesting, and adds more interesting choices I'll be solidly behind.
The two things that I need to hand wave away with Starmade is the power reactor system and how the best ships are literally solid chunks of systems.
I do have reservations on your heat-box idea, I'd worry it could be too restrictive on being creative with a ship's overall shape. However, depending on options for mitigating heat, that may or may not be an actual concern, if one can add enough cooling systems to a reactor to collapse the heat zone to within a few blocks of the reactor, it would be a non issue. I do really like the idea of adding mechanics to encourage players to design complete reactor that in turn need to be protected and cooled.
A balance between forcing a heat box, and just making system crammed ships automatically and decisively better would be to tie heat dissipation to the exterior and interior surface area of blocks next to empty space. Ships with a more open design could dissipate heat more easily and require less cooling systems, but solid ships could devote more systems to heat dissipation and retain a higher efficiency by size in exchange for more more expensive and possibly more vulnerable heat dissipation systems. Yes, I know this system could be open for misuse by simply having long empty hallways added to a ship, but they'd still be trading potential blocks for easier heat dissipation. Finally, how the heat exclusion zones of turrets with on board reactors and shipboard reactors interact would need to be figured out.
Another question to ask is if and how does heat effect rail systems, or cargo systems? If heat does not affect cargo/rail, the heat exclusion zone on a ship would be a great place for a cargo bay or hangar/flight deck.
One could also have different tiers of power generation blocks, starting with easily crafted solar panels, to fission, to fusion, to Matter/Antimatter, to artificial singularities and zero point energy modules depending on how many scifi power generation tropes one would wish to bring into SM. The more powerful power modules would obviously require more resources, but then have other attributes that would make them better/worse for different ship sizes.
There also has to be some in game way to tell what kind of power generation you'll get at what levels of heat production. While I'm sure it's possible, I can't think of a good way to completely remove the energy per second stat from the player hud in build mode and still have the information one would need to build an efficient ship.
To be completely transparent personally, this system would work great in how I already build ships. I tend to build in the zone between pure RP ship and killer PVP ship. All my ships have a few small decks of interesting crew related rooms to wander through, and simply shifting the decorative reactors I already have forward and into the middle of my engineering deck and reworking that deck would make my ships if not easy, at least straightforward, to convert to the proposed changes.
I supposes the big question is if the current difference in performance between pure solid PVP ships and RP ships is desirable or not? I personally find RP ships far more interesting than PVP monsters. I'm not entirely convinced adding a small to medium amount of interior really hurts your ship all that much, even under the current system. Finally, If building ships in this game was simply just an exercise in man/maxing a stat line, I would have quite playing a long long time ago.
