You might consider examining skill sets somewhat differently than from what I have seen above.

From a pilot's perspective you would need to not only be aware of the capabilities of your ship but you would also need to know how to navigate around or through hazards, dock at starports/motherships safely, land and takeoff from planets of differing environments. Depending on the types of hazards in game you might develop skill sets that might enable navigation through or utilisation of...for example the ability to weave through an asteroid field or slingshot off planet or land successfully on an asteroid with microgravity are possible ways you might explore with regards to travel shortcuts, fuel savings or opening access to previously inaccessible environments.

From an engineering perspective: You may not always have the parts on hand to make repairs by slotting the right spares in which means jerryrigging fixes utilising whatever is at hand. Oftentimes you might find yourself in a situation of needing a tool or a machine to be created to service a particular unique need...for example a vacuum hose to suck up some exotic atmospheric gases from a planet you cannot land on in order to replenish your fuel. Or perhaps marrying alien technologies into your spaceship in order to utilise them or simply being able to determine whether the unusual piece of alien technology is something more than a toilet seat.

Combat skill sets you might consider from the perspective of not making them anything more than simply a license structure for example; The (legally obtained) planetbuster bomb might require you to have qualified and met an incredibly stringent set of conditions but in meeting them you would have a better understanding in the implementation of the bombs as opposed to a "pirate ship" with their (illegally obtained) planetbuster bomb i.e. inline with this link. Licensing requirements might also lead to trade opportunities (either as a company salesman or gunrunner) with regards the selling and obtaining of combat related equipment.

You might also wish to consider such things as a master trader tree by where you develop skills associated with trade, languages, legal knowledge, diplomacy. Dependant on your skill level and reputation established you might open previously inaccessible markets, receive more comprehensive trade reports i.e. be made aware of shortages or surpluses. Other aspects might be ameliorating offended aliens by your drunken crew's antics of urinating against the sacred wall of kybosh.

Hope this helps :)

One game i played had a skill called "learning" by leveling it up you unlocked other skills,

then again a player could also spend everything on leveling up a few skills which are unlocked in the first few learning-levels

We are happy how it turned out for a piloting and engineering trees, but combat tree... so far we can't make it any good. The problem is - we don't want to group skills there by weapon types, it's just too simple, plus it would lock players to only use one weapon type. But doing it otherwise - we just can't make it any good/interesting/balanced.

Hmm, how much do weapons themself differ to make the players choose different types ?

You could have different skills affecting a multitude of weapons;

for example:

one skill to boost all weapons made of iron.

another skill to boost big weapons.

a third skill to boost long range accuracy.

A player choosing these 3 skills would most likely fly around with a big iron long range gun,

but he/she could switch to a short range big iron gun for a certain mission, missing out on his/her long range accuracy skill but still using 2/3rd of their weapon-skills.

Thinking further, a lot depends on whether or not you'll allow respecialization of your character skills.

That's actually another important point. We are not going to allow respec. Because these skills pretty much determine your character "class". I think you can agree that if you were playing a warrior and suddenly decided to switch to a mage it would be just too simple. Plus it is a hardcore game and your choises must matter in a long term.

So if a player makes a few silly choices at the start of the game he/she should pay for it until he/she makes a new character ?(which will happen)
You don't have to allow "free" respec, btw. Players can have to do missions or pay or whatever to respec, this can be made expensive enough so that a player will almost never fully respec to another class, just finetine stuff.

If need be, you could give the ability to "forget" one ability(maybe over time) whenever a new ability-point(experience, whatever it is called in your game) is earned by the player.

Yeah, the problem with skills is that a player doesn't really know what they do, or whether they will actually like the skill, until they've chosen it. So having a way to respec in these type of games is a good thing for limiting player frustration.

I would try making the different tree branches be based off of playstyles, so that a player can have some idea of what branch or branches they should try going down. If one is all about maneuverability, one is about dealing damage rapidly, one is about high alpha strikes, one is about stealth, the player can then decide they want to play a stealthy ship with high alpha damage, or a fast ship that has high alpha or a fast ship that deals rapid damage, etc.

Well, it looks like you have your work cut out for you.

Well, I guess so :)

You say your skills will define your class in an organic way, so it would make sense to have the trees arranged in such a way that they define an archetype.

Yup. That is what we are trying to do.

Could you offer synergy between the skill categories, so that your aptitude for more maneuverable ships would offer a bonus to the effectiveness of cannons that are aimed by maneuvering the ship, or would you just let the player's superior ability impart that bonus in the practical sense?

It is not that simple unfortunately. There are not that much possible combat skills that we can realistically implement. Mostly increasing different stats. Creating something wholly new is time consuming and not always worth it.

Without knowing what the individual skills are, I can't give much specific feedback on their organization, but this is a fun topic to think about, and I wish you luck with your design.

Thank you :) And yes, that is certainyl a very interesting topic!

You might also wish to consider such things as a master trader tree by where you develop skills associated with trade, languages, legal knowledge, diplomacy.

Yes, this is another interesting idea. We have skills for basic trading and skills to get services at stations for cheaper. But we also have skill for persuation that the player can use in dialogues. Right now it works just by providing extra option when talking to npc. I was thinking of possibly making it more interesting in some way.

Dependant on your skill level and reputation established you might open previously inaccessible markets, receive more comprehensive trade reports i.e. be made aware of shortages or surpluses.

But how is this going to work? The character can't just "know" that. He will have to ask that information in a station or somewhere else. But in that case why can't he ask that without skill?

Hmm, how much do weapons themself differ to make the players choose different types?

Well, we have weapons divied by size (small, medium, heavy) and type (energy, ballistic, missile). But inside each group there are many different weapons. For example light energy weapons could be: lasers, pulse lasers, plasma cannons, ark dischargers, etc.

You could have different skills affecting a multitude of weapons; for example: one skill to boost all weapons made of iron. another skill to boost big weapons. a third skill to boost long range accuracy. A player choosing these 3 skills would most likely fly around with a big iron long range gun, but he/she could switch to a short range big iron gun for a certain mission, missing out on his/her long range accuracy skill but still using 2/3rd of their weapon-skills.

That is interesting possibility. But in that case how would you suggest to lay out the tree? What main branches would you add?

So if a player makes a few silly choices at the start of the game he/she should pay for it until he/she makes a new character ?

No, the tops of the trees are generic enough and usefult enough that it would be okay for anyone to pick it. But the more down the tree you go, the more specialized skills become. So, you will understand the usefulness of each skill before you can actually learn it. But yeah, you have a point, I can't deny that.

I would try making the different tree branches be based off of playstyles, so that a player can have some idea of what branch or branches they should try going down. If one is all about maneuverability, one is about dealing damage rapidly, one is about high alpha strikes, one is about stealth, the player can then decide they want to play a stealthy ship with high alpha damage, or a fast ship that has high alpha or a fast ship that deals rapid damage, etc.

Yes. That is the idea. I don't remember if I mentioned it already, but for example for piloting tree we have following main branches:
* fast combat - for people who plan to have fast and maneuverable ships.
* slow combat - for people who are interested in slow and heavily armored ships.
* civilian - mostly for these who are interested in trade, engineering, mining, etc.
But these are only general archetypes, you can of course mix skills for different branches to create something that you would like yourself.

Also. It might not be the best place for it... :) But if you people are interested to try the game we are looking for people to be in the Closed Alpha Test team.

In that case please follow the link below:
http://forums.atomictorch.com/index.php?topic=21.0

I would go for a set of static skills which you can upgrade as the game moves forward (like precision in aiming, trade bonuses etc.). The extra special effects like abilitiy to construct a ship would be accomplished through items and consumables. I think that makes the game easier to design, as you can place the "enablers" in maps/planets etc. rather then a vague upgrade of player character.