Equalizer 1. Power and Ammo production placement
The missiles update should help at least a little with these problems, since most of the missiles can be carried longer distances. They'll be highly explosive though and will benefit from sharing power/ammo with other parts, so internal design will hopefully still matter.
Conveyors are also getting significant buffs in 0.14.5, which should also help somewhat.
Upcoming larger reactors will also change this significantly. Depending on just how big reactors are, there might be situations where you only have 1 or 2 centralized reactors on a big 1mil ship. AFAIK the current plan is for them to produce larger batteries which will be more crew-efficient than the current reactor.
You know, that's a good point. Why do shields have that exclusion zone, since 99% of the time they're used exactly like a 2x4 part. The exclusion zone is just kind of.... there. I'm not sure what a solution is, or if any is even needed.
Regarding thrusters, I kind of agree with you but I'm also not sure what the solution is. Just increasing the exclusion zones breaks existing designs, and viable internal thrusters isn't necessarily a bad thing.
Larger reactors might help this a little, since you'll want to put your quarters near the (hopefully centralized) reactor for faster response time. We'll probably have to wait for crew 2.0 for major changes though.
Equalizer 4. Ship shape (or the tyranny of surface area)
0.14.5 missiles can probably improve this, since some of them they are cheaper to store than to produce (missile storage might be a good way to fill internal space), and they all don't take much forward surface area (even the unguided ones)
Hopefully the tractor beam (which IIRC is going to be an internal part) and upcoming larger reactors can help some as well. Blink drive/multiplayer FTL and new control room types might help a little with surface area too, depending on how much space they need.
Equalizer I think the importance of logistics / what good logistics looks like currently isn't made very clear in the game
(I am looking at you inefficient built-in bounty mode ships).
Yeah, I fully agree. 80% of making a good ship is internal design, and the built-in ships will need a big revamp to help new players learn, probably when parts are finished and walt gets around to building a dedicated single-player mode.
Though I think it's important that if internal design does get more intuitive, we need to be careful that it doesn't get so intuitive that it becomes easy, or simple. Internal design is one of cosmoteer's main attractions, and if the learning curve gets too flat then players will feel like there's nothing to master. It feels amazing when you learn to stop making basic mistakes and your ships triple in strength, and IMO that's an important joy to keep.