Due to thread necromancy I'll take this chance to put my two cents in, and actually give a general idea of what I think about the current skill system.
First boarding so far feels a lot like release day Diablo III, by being completely RNG related, and when you actually got a set piece you wanted, it rolled main stat of a different class. It was not fun, required a lot of grinding, and it was probably geared towards the use of the auction house. It was rewarding though I probably still have my Inna's belt stored in a mule character. Blizzard "fixed" this by making drops weighted, catered to what you play, and giving you a reliable way to get the items in the form of greater rifts.
I could see this working for Starsector, as an example I usually prefer high tech ships and energy weapons. After destroying a fleet with some mixed ships and weapons, the game could detect what I'm using and give me weighted loot, so maybe tactical lasers get a doubled change to be part of the loot in contrast to machineguns (since I don't have a ship that can use them), and for boarding the wolves in the fleet get preference over the lashers, even further the game could detect that I have no cruisers, despite attacking fleets which have them, and offer me to board one (if you currently have the means to do so)
This would work, better what it currently is, but it is also horrible by forcing you on a set path...
Honestly, I think the system needs to be scrapped and then reimplemented, and actually be tied to newer systems, specially salvaging. So I'll propose something, based in multiple stuff I've read while lurking on the forums, I'll do so by presenting a fictional after combat scenario...
Incoming wall of text, open at your own peril.
Spoiler
So my fleet has just defeated a Tri-Tachyon fleet, as soon as the battle finished I get presented the classic loot menu we all know and love. I get the chance to pick up supplies, miscellaneous items and some floating weapons. This is also where the first point of frustration happens in the base game as I might not get the chance to loot that sweet plasma cannon (in this case I might actually reload and repeat the fight if it was easy, if it wasn't well I would get frustrated a bit; heh, I've even done this just to get some tactical lasers).
Until now, no changes, but after selecting your "quick" loot you get presented a screen with all the disabled ships in the conflict, including yours. Here the game would assign a first pass of RNG and give every ship a visible indicator of how intact it is and how strong is the surviving crew. You would be presented the choice to either leave, scrap some of the ships for extra loot (how nice, a second loot pass where I might get the plasma cannon I wanted) or try to board and salvage some of the disable ships which would need marines/crew, a ship capable of performing repairs, and maybe tugs.
No big changes yet... not really, I'm proposing that every single ship is made available to be "captured", however how costly (marines/crew/maybe even ships) and how long it takes me to do so is what the RNG pass controlled.
I choose to scrap the ship which had the plasma cannon and to board and salvage a medusa. At this point if I was not prepared to do this I would get quite costly, since I didn't have a boarding capable ship (a dedicated shuttle, with a specific hull mod), or a lot of marines, I sent my own medusa and boarded with crew, they get overwhelmed and I get a new popup menu, the ship is going to self destruct, either I send more crewmen and risk my ship to get damaged in an explosion, or decline and accept my loses. Since the game gives me an approximate chance of being successful depending on how many troops I send, I decide to maximize my chances up to the maximum it would allow me, this time I send an overwhelming number of crewmen, as the game gives a 80% chance of success. After committing to board again, a new window appears and informs me that the enemy crew was eliminated and my loses, it also says that the target ship was heavily damaged... not good.
Now I get back to the disabled ship screen, I can see now that the medusa I boarded has no crew strength left, and is ready to be repaired, it's intactness dropped severely though. Considering I was prepared to repair my own ships by having a couple of tug and a salvage rig, I decide to repair the medusa and one of my own ships that was disabled. The game informs me that due to my skill level and fleet composition to scrap 1 ship, repair to moving condition my wolf and the medusa I would need to spend 5 days in total on the debris field. I take accept.
Back to the campaign map, a small transient feature has appeared in the system right below my fleet, a large debris field, if I click on it with my fleet I get back to the disabled ship list and I can order some changes, but I don't.
1 day has passed and the ship with the plasma cannon was scrapped, because my salvaging skill was low, and I set the salvage rig to repair the medusa, I just get some extra supplies, and a tactical laser, there are 4 days left in the counter to repair the medusa and 3 for the wolf. 2 more days pass and my wolf is back online, but since its intactness was low, it became a (D) variant, I'll need to repair it properly on a friendly base (either one of my own outposts, or in Jangala because the Hegemony is favorable to me and I've invested some points in a diplomacy skill).
Also on the third day an independent scavenger fleet appeared, they kept their distance since I was first, they have a good relationship with me and my fleet is bigger.
On the fourth day a new Tri-Tachyon fleet appears, since I didn't scrap all the ships some of the still living crew manage to send an SOS, had I had a high tech skill in communications I might have been able to detect it before. The fleet is larger than mine, and meanwhile I could take on it, my fleet is low on supplies. I decide to leave.
The Tri-Tachyon fleet pursues me for a while, and as it does so the independent scavenger runs to salvage the now medium sized debris field, some of the less intact vessels left unattended had exploded on their own, some of the more intact ones with a strong crew presence managed to repair their ship and left, I allowed them since I didn't want to wasted CR by engaging them.
As soon as I'm somewhat far away from the site and the independent started salvaging, the enemy fleet returns to the debris field, scaring the scavenger away. I keep watching, 2 more days pass and the debris field is gone, the Tri-Tachyon fleet repaired and scavenged the rest of the fleet, I check its composition it now has a medusa (D).
I decide to engage it, after all now my ships are back to full CR and I'm better at combat than the AI, even if I don't take into account my combat skill, and more importantly I still have surplus redshirts.
Well that's the end of my ramblings. In my dream game that's how I would go have it go. Despite not having the proper skills and marines, I still manage to run a somewhat efficient salvaging operation by using skills that are less related but still useful, and supplying those that I lack with ships. I know it would mean some big changes, but I'm pushing for more integration between combat, the campaign map, skills and actually more equally valid alternative paths to do something. I've never really liked when games makes something impossible because I didn't pick some specific skills. Well I guess it's fine for shorter non sandbox games, in those I do a second run with a different setup.
Apologies for the large wall of text, and I hope this has some internal consistency and makes enough sense, keep in mind english is not my first language... heh, 3 pages on word, well I had fun doing so though.