I feel like this could be solved by better AI
That is true however I have decided to propose a single tickbox for several reasons. First it will take much less coding. Second even though C# Aurora will be much faster I'm still worried about resource usage. Third at the beginning shipping lines have only enough money to buy a couple of ships and they usually buy a single type of ship, so they may still end up failing without subsidies as they usually build one type of ship at the beginning.
I think the problem could be far better solved by limiting all Civilian Shipping Lines to a single category of ships (so cargo only, or colony only, or luxury passengers only ((Also, please bring back Luxury Passenger Ships.)) or fuel harvester only, etc.) That way, only the types of civilians actually being used would make money and thus build more ships.
The reason I dislike the idea is due to potential clutter. In many cases I found myself using basically no colony ships, either because the nation was small or because I had large nation that didn't need to move people around for both practical and RP reasons. Not only that but fuel harvesters generate almost no money so I'm not even sure you could have a shipping line operating those exclusively. This would lead to whole lines being essentially useless but still cluttering the UI.
Also the lines currently do build liners (you as a player can't build them though) and they are absolutely broken, generating insane amount of money in some circumstances. Too bad lines build very few of them.
1. Please allow us to modify characteristics of various stellar bodies or, even better, add custom ones.
2. System generation algorithm should be modified in my opinion.
A dialog where one can select several parameters as to a rough category of system that should be created would help much.
I have to admit that a simple screen to, for example, select number and general type of bodies (dwarf planets, terrestrial planets, gas giants, asteroid, comets) would already be a vast improvement, and something much easier to code. Would definitely be happy with just that. By the same token I'm an empire builder and a full scale customisation would allow me to, for example, simulate turning gas giants into miniature stars, or towing asteroid to a new position and turning it into garganutan fortress (though now that PDCs are gone it will no longer be possible). For that matter with the ability to fully customise location and so on of objects and if we had PCS back it would be very easy to simulate having a death star.
I think the civilians will be better in building new ships, depending on the needs of the empire. Steve wrote about that not so long ago. Although, being able to "select" which areas are made accessable for civilians would be a) nice, and b) make it easier to simulate different kinds of societies.
I've checked the official changes list and all it said about civilian shipping lines building AI is that they will be building more even numbers of freighters and colony ships, which is exactly what is causing me problems right now. It's possible something was mentioned in other topics, but I haven't seen that.
For 3. I think ECM will at least alleviate the problem somewhat, as loosing 30 or 40% interception chance is quite painful, and ECCM uses up 25% of a 1 MSP countermissile.
I'm not sure it will help as we will now be able to build fractional size missile launchers (1.1 HS for example) which will allow construction of larger, but still far smaller than 2 MSP counter missiles. This makes ECCM not that difficult to build in, while still leaving very, very large space for agility. In fact those fractional launchers may even make the matter worse as it may end up being possible to build an anti-missile that is 1.3-1.6 MSP that has 90% interception chance or so. It's difficult to say without having access to the finished game, but this is what I fear.
4. I think it is a serious problem. It could however be fixed with making box launchers larger.
Per msp missile size if you have 3 HS giving you 2 launchers + 1 HS magazine you can fit in 16+2 missiles at 80% efficiency. The same size in box launchers fits you 20! missiles, more than the re-loadable solution.
I'm afraid you forgot that capacity has to be divided by missiles size. 1HS magazine will give you 16 capacity allowing you to carry five missiles, for a total of seven. However I would argue that your example isn't really that good, for in that situation you could five only three times per launcher. If you build them to fire 7+ salvoes magazines are much more efficient way to store missiles than box launchers. So box launchers are already a tredeoff - lower total ammunition capacity in exchange for firing all of it at once.
As for gauss cannons, one possibility to make smaller missile sizes viable would be to limit the amount of shots that can be fired on the same missile.
I"m afraid you're forgetting "bonus tracking vs missiles" tech. Gauss cannons are very, very accurate and it's very rare for them to need to fire more than two shots to take down incoming shipkillers of equivalent technology level. At least I think so, can't be bothered to do the math right now.