Skills etc: this is starting to get a bit off-topic in that it's dominating the discission in this thread. Lots of stuff to consider here, but it's also re-treading some familiar ground, so I'll cherry-pick a few things to respond to and ask that we keep the rest of the thread more on track

... But if an ally is fighting 3 to 1 and I have a couple of frigates nearby I can give my best shot at turning it around. Not to be callous to my allies, but when I'm not directly paying for their replacements, a brutal fight that can come down to only a handful of survivors per side can still be something I gain from, where if I did own the whole fleet, the best case scenario would still cost a fortune to rebuild from. I'm hoping this means we get more fights like that.
Yep, exactly.
I think its fundamentally unsatisfying in a game focused on flying our spaceship and blowing up enemies for the individual ship boosting skills to be suboptimal - the player should not be worse than the officers at boosting their own ships unless the officer is higher level than the player. "Officer Envy" is real and bad.
I think the main thing here is "officer envy". Which gives me some other ideas, but in the name of not contributing to derailing the thread further...
I like the notion of "masteries", or something of the sort. Something like, a fleet commander who used to be (and still is) an excellent captain can make use of that knowledge to revise fleet SOP or train his subordinates and their crews accordingly?
Yep, that would be the notion, if that's the way "masteries" went.
More on topic of far flung outposts, I think it would be cool if there were a few small, independent colonies strung out in the outer systems that the player could find. I often see groups of scavengers all mining the same resources in a far off system, so if they had some hidden base that I could tail them back to and then trade with it would be really cool. And then it would be on my map to plan future expeditions around.
It would make things feel a bit more alive. On the other hand, it would upset that "far away from any civilization" feel the outer sector has at present.
Yeah, I've been thinking about that too. Could be really neat to find an existing colony - either one you can govern yourself, or just reconnect to the core worlds.
Alex, would it be possible to add a feature allowing you to rename Officers and Admins? I always had fun doing things like that in DF and Rimworld and naming various sims and dorfs after my online friends and whatnot, thought it'd be fun here too.
I'll keep it in mind! Not a priority item but might be able to work it in at some point.
Will we be able to build a shipyard of sorts on these colonies, to construct various ships and weapons? One of my biggest gripes with the mid game is after raising your reputation and killing a few pirate bounties, going from planet to planet to see if they've got any new weapons you can use, or in one unfortunate run no one was selling sunders. It would be great to invest in your colonies to being able to craft ships and equipment, to have some better control over the fleet you use.
I would imagine so, to some extent, but the specifics are very much TBD. I could see something like "you find a blueprint for X and now your heavy industry/orbital works can produce it", for example, but no commitments on the details.
http://fractalsoftworks.com/forum/index.php?topic=13018.0
an idea for how a new reputation system could work
Hey - yeah, I did see that! In brief: I get the idea, but I think it suffers from "makes sense behind the scenes, total pain to actually convey to the player" issue. You know what I mean? "Your Hegemony reputation in Corvus may or may not change by a couple of points in one or the other direction in a few days, which may or may not be enough to enable|stop you from being able to buy a ship that requires a certain reputation level" etc.
(Ironically, my first internal stab at the reputation system design looked very much like this.)
Firstly, I want to ask - when Alex says Combat should be weaker because it's cheaper, he means the idea that you would use less ships because you rely on your flagship more, correct? If that's the case, I don't think that's correct. I enjoyed Starsector before the combat skill changes and I still thoroughly enjoy the game! However, as it stands now I wouldn't call a combat path cheaper. If you want to face end-game fleets, it's impossible to do a combat-focused player build without investing in a large fleet or investing in a very long, drawn out battles.
Ah - what I mean is it's cheaper when it's smaller scale, and if it was also cheaper on a larger scale, than that would be its own problem. So, we're pretty much saying the same thing.
I had that happen a lot when playing as the Knights Templar using only those Crusader cruisers, trying to save on supply costs by only deploying a cruiser. There would only be like two frigates and one destroyer left, but they would refuse to fight until their CR got low. That was a pretty special case, what with playing a mod not even designed to be played by the player, but yeah it's really frustrating.
Yeah, I've got a TODO item somewhere to help address this. It's a gradual process, weeding out these special cases - it's gotten better than it was before, and hopefully it'll get better still.
When you say "I want to have separate trees for combat and fleet skills," I hear "I want a combat skill build but I'm going to choose the best build available to me, and that build's a support/utility role with officers doing the actual fighting. So can you please force us to get some combat skills so that I can play how I want to without feeling like I'm using a sub-optimal strategy." But for me, a support player by choice, that sounds like being forced to take half of a build that I really enjoy and put it toward a playstyle I don't much want.
I think that's really well put and nails down why I'm not a fan of the "two skill pools" idea - it makes a hard assumption that the non-direct-combat skills aren't fun, and that's a subjective evaluation, even before you consider how having those indirectly changes your combat experience.
How about a stat like "intimidation" or "reputation" that grows with each point invested into combat skills. It would give a bonus to certain negotiaion related things like bounties, probability of smuggled goods being found or even prices of fuel and supplies.
It even makes sense that personal combat/badass skills that are not directly related to your qualification as a leader are still recognized. Just think of Teddy Roosevelt.
I've thought about stuff like that, or even tying that into aptitudes. It's just hard to think of that as a balancing factor, because "certain things" seems like it would inevitably end up as "a few random things here and there that are hard to properly consider as a whole", if that makes sense. It could be a neat element of the combat skills (or of something else, such as just winning battles when outnumbered), but, again, hard to see as a balancing factor, especially as it'd be tough to convey to the player beforehand, i.e. when they're making their skill choices.