https://endless-sky.github.io/plugins.html
https://opengamemods-group.github.io/ES-Mod-Share/
Creating a plugin (mod) for endless sky is super easy, and that's what you'll need to do if you want to share your tweaked ships.
I was thinking of mines as an engine-space weapon. I made some and proposed them in this thread on the mailing list: https://groups.google.com/forum/#!category-topic/endless-sky/content-creation/OmxQSFlssyg
There are some missions where you finish them and then there's a time delay until the next one is given to you, but from what you're describing I don't think it's one of those. How many game days has it been?
You might have a broken save file, you could try posting it in the troubleshooting category at https://groups.google.com/forum/#!forum/endless-sky
Interesting list. For all of these it would probably help if you'd offer an idea about how it could work. For example, on #2 there could be an Engineering Bot outfit that you install that can do in-flight equipment swaps.
If you want to make sure any particular suggestion reaches the developers, post it on the Endless Sky Google Group (there's also more discussion there). https://github.com/endless-sky/endless-sky/issues
Re number 4, it's fair because they aren't docked with the ship, and you might be in the middle of a raging battle so how would you get gear from that ship to one fighting on the other end of the system? But if there was some way to have some or all of your escorts board "with" you than I could see this. It would muck up balance I imagine, and even worse if you allowed crew from other ships to take part in combat.
5 - Switching flagships at any time would solve this, but again would throw a lot of existing balance out the window. You wouldn't have to craft your flagship as thoughtfully as you do now, not sure what to do about that.
6 - You know that if successfully demand tribute you can grab an already inhabited planet? Not that exciting, what exactly do you want to do with your planet?
7 - Destroying asteroids would be satisfying. What if each hit had a very small chance of kicking off a chunk (equal to say 10-20 units) of metal or heavy metal you could "board" to pick up? (or tractor beams, but that's a whole 'nother conversation)
EDIT: responded to more of them EDIT2: updated info/links for bugs/suggestions
A lot of mice are programmable nowadays, if you download their optional drivers. You could set up macros to automatically press those keyboard controls when you use those mouse buttons, if your mouse allows it.
If not, you could use AutoHotkey to rebind those controls. It's dead simple to set up a macro to rebind keys and mouse buttons, and have it only do that while Endless Sky is in focus. They have good documentation and a helpful forum if you have any trouble. That'd certainly be easier to learn than modifying the C++ code, in any case.
The Carrier is a Republic ship, and it technically requires ship licenses that aren't in the game yet, so you can't buy them. They're the ones that fly around dropped drones all over the place. You've probably seen them without realizing it, since they look just like other Republic ships, just slightly bigger. I'm not sure if you can board and capture them or not.
The Shield Beetles are alien "Hai" ships. They're off in a different part of the galaxy. This link isn't a great picture of the map, but in the upper right you can see the system Ultima Thule. Head there and you'll be able to find your way to the Hai systems. You'll need pretty good fuel reserves, it's 6 or 7 jumps between planets you can refuel at, but it's no problem for a Bactrian. You'll have to land on their homeworld to buy a Shield Beetle, and to do that you'll have to bribe them (Shift + T to talk to a selected planet). They also sell some pretty good shields you can equip onto any ship.
I was wrong. Suggestions (and discussion too) go on the Endless Sky Google Group. https://github.com/endless-sky/endless-sky/issues is for bugs
I haven't really tried the 3d style, so I can't speak to that much, although, I'll just add that it's a lot harder to understand what's happening around me in 3d space, and targeting is a lot harder.
ev-like games have some things in common that I love (perhaps I'm biased because I grew up with EV):
inertia. This is key; it makes it feel like I'm really in space. It also adds some nice combat options.
trading and combat in an open world - I want to be able to choose what I do, and when I do it
rags to riches. You start in one of the smallest weakest ships in the game, and through trading and fighting, you can become one of the most powerful forces in the galaxy, but it takes time, and you have to work hard first
EV in particular has one more, which is:
SpaceRPG3 has all 4. SpaceRPG4 does too, to a lesser extent, but also, 4 is richer and more like endless sky.
EV Nova was made by Ambrosia Software, and you can grab the free trial right here. I'm not sure how long the free trial lasts or how far you can go with it, but hey it's better than buying it and hating it! Ofc you can also buy if from that same link, but I would try before you buy, since it really suffers from old-game syndrome.
the Wanderer storyline is MZ's, and in his most recent blog post he said again that he wishes to continue it:
https://endless-sky.github.io/2020/05/01/stable-release-0.9.12.html
so I'd discourage you from writing for that storyline because of that