Had a read through the latest blog. So far, it seems pretty fun and it gave me a few ideas.
Maybe instead of a random chance to board one ship, boarding could be one of the options after winning a battle (being mutually exclusive with salvage and that other stuff). You'd then
get to choose which ship you want to board, and you may pick one that can't actually be repaired pick one or more of the disabled ships you want to board (could display estimated odds of repairing the ship). EDIT: I should clarify, it would pretty much work the way you described what with random chances and all that, it would just be worked into the existing framework a little differently. It would also add a little more risk/reward (do I choose guaranteed extra loot, or a chance at a "shiny" new ship?).
Lore reason could be that the surviving crew on all the disabled ships do their best to bring their systems back online. If they're successful, they can break away while you're boarding the other craft. If they fail, they may sabotage whatever's still usable out of spite for you. In both cases, it means less salvaged loot than if you choose to scrap them before they have the opportunity to do either.
I also couldn't help but notice that you mentioned something about looking into fighter mechanics... so I'm going to shamelessly *** out this thread here:
http://fractalsoftworks.com/forum/index.php?topic=5910.0. I quite like the idea I came up with about fighters costing CR to be repaired and, most importantly, rebuilt. To summarize my idea, a destroyed fighter wing isn't necessarily gone. As long as it has enough CR, it can be replaced. However if the fighter wing is destroyed and its CR is too low, it's permanently gone.
I dunno, I just feel like it's too easy to completely destroy fighters. And frankly, it doesn't make sense that I can have 1 Wasp remaining and have it be restored to full strength, but the moment that last Wasp is destroyed it's gone for good. With CR, though, you could make each individual fighter have a specific CR cost to rebuild/repair it. For example, reconstructing Wasps could cost 4 or 5% of its CR per fighter. Reconstructing Xyphos(es?) could cost 15% of its CR per fighter. Lots of fun stuff you can do with it.
EDIT: Lore reason could be that as long as you have one full fighter, you can use that to make copies up to whatever the DRM allows you to keep in storage. Once the last one's gone, no more copies since there's nothing to copy. How many you're allowed to have deployed at one time is also constrained by the DRM. It's a bit contrived, but it makes a bit more sense than what we have now =p