Your notion that the game will be so delicately balanced that your skill selection will determine if bounty missions are profitable or not... Sound so unfun 
I really hope we don't end up there. More power to you if you like it, but we'll just have to agree to disagree.
Your notion of a game that is so untuned as to provide little incentive for player experimentation, roleplay, and specialization, and hence little replay value sounds fun to me...for about 2 hours until I get the best ships and faceroll the AI, and then never play the game again. To each their own I guess.
Besides that, your example seems a bit contradictory. Right now, anyone and everyone can salvage most things and if you can't salvage something then you blow it up and salvage the debris instead. As such salvage ships are good for everyone. Further more, if you follow PCCL's example and quintuple supply costs and/or follow your example of locking down the economy more (I think that's what you were implying. Apologies in advance...), flying 4-20ly to the nearest bounty without storage and fuel ships and industry/leadership skills to reduce those costs will be harder and less efficient.
Everyone can do everything right now because the economy is so out of control it doesnt discourage it. Doing a bounty mission with a dedicated combat fleet and high combat spec will make it much more profitable. I dont necessarily mean combat tree spec, but spec to make yourself efficient in combat. You can currently be efficient in combat by: 1) Combat tree spec (strong player ship requiring fewer support ships), 2) Leadership focus (strong carrier fleet requiring fewer combat ships altogether), 3) Industry focus allowing you to throw large amounts of trash ships at the enemy for reduced cost. If you try to do that bounty with an unfocused skill selection that makes you inefficient in combat, and carry around a bunch of ships that don't contribute to your combat ability to boot, you will easily blow through that mission reward in round trip travel, deployment and repair costs. But there are so many other opportunities to make stupid amounts of money , the inefficiency doesn't hurt. It doesn't hurt to lose ships, it doesn't hurt to waste gas and supplies, and there are no difficult choices to make in ship selection because ships are cheap ( free even), bank accounts are huge, and the game throws so much cash at you you dont have to make any good decisions.
Maybe what you were going for would be well served by having faction specific opportunities. The games I think told really good stories and had good replayability involved aligning the player with different factions each play through. Today you could go all Pirate, and that's pretty dope. Go rob people blind. Another play-through you could be the bounty hunter and chase down the pirates you used to play as in a previous life. Be a TT shill or Hegemony officer another day. Skills have nothing to do with it though.
We agree in principle here. Yes, this is the game that I ideally want. I want the game to be essentially like a 2d version of the egosoft X games (not Rebirth, we dont talk about that one). I think that's a lot to expect from a lone independent developer, so I'd be content with something closer to Sid Meiers Pirates in space, with modding to pick up the slack.
Those games dont feature a RPG-like skill tree at all, so I wouldnt miss it if it were gone--allowing the player to define specializations for themselves, as long as economic factors made it impractical to try to do everything at once. But if there IS going to be a branching skill tree, it should actually branch the player into different playstyles, or there's no point to it.
Where we disagree, is that I think the game has the basic framework to support this already, with a bit more fine tuning. My playthroughs are all very specific along certain themes. Trader/junker pirate/Bounty Hunter/fleet admiral, etc. The nature of the combat encounters I seek out varies in each one, as a result of the logical playstyle. Combat is a part of each playthrough, but not each playthrough is about knocking out capital ship battle fleets in bounty missions. Some are about running from patrols and going dark to avoid scavengers, or carrying just enough military power mostly in the form of combat frieghters to survive redacted encounters while salvaging huge paydays. I really look forward to the outpost building, and opportunities to make economic playthroughs more viable.
