Thanks for the guide Thaago!
I'd bet there are so few mission chains in mods right now because most modders know that system/API isn't finalized and don't want to rework everything later. And writing takes a huge amount of time as well as many have already said.
There were a few deprecated changes to how quest-making code works just between .8 and .9 and I would expect there to be even more in the next update as Alex fleshes out how he wants that to work under the hood. Bar events may change as well since if the past is any indication there are always at least a few small tweaks in the next update from one that introduces a new feature.
I can't wait to see what people eventually come up with once it's more stable though!
To the OP: iirc I spoke with Alex years ago about the potential for ground based combat mechanics based around the current combat engine. (I was very technically naive at the time to think that would be in scope, heh.) But not only is that extremely time intensive to do, it creates a bit of dissonance in the game's natural flow of activities to saturate it with what would boil down to mini games everywhere. Even assuming making them optional as a solution for personal tastes could be done in all cases, it would be difficult to maintain quality in the overall campaign rig because it introduces concerns like: Space combat is fun! Ground combat is boring. But now half the game is ground combat, etc.
I personally would love stuff that really effects the in-game factions and ties into the reputation system more. Stuff that showcases the factions' personality and identity and lets players directly interact with iconic characters.