Ugh, skills for Elite kind of game. That would be tough indeed... The core poblem is that's an "arcade" game (you fly the ship, aim and shoot), and for these games artificial skills (no player's skills) are usually not working that well...

I can think of station skills (like buying bonus, negotiating contracts) and repair skills (repairing the ship during battle, prevention of system malfunctions) maybe also passenger capiacity skill (as a skilled captain you are able to cramp the passengers better and therefore take more of them on the ship :D). But for combat, I can think only of unlocking weapons (require X to operate weapon Y).

I guess I was not much of a help :)

Ugh, skills for Elite kind of game. That would be tough indeed... The core poblem is that's an "arcade" game (you fly the ship, aim and shoot), and for these games artificial skills (no player's skills) are usually not working that well...

Well, in our case it plays like EVE in 2d world. So, there are a good number of skills actually. The problem is making it into a coherent system... which is hard.

I guess I was not much of a help

Well, anything helps :)

As Acharis notes, the space for artificial skills is limited; probably too limited for ambitious, character defining skill graphs.

I think there's a replacement for artificial skills that might or might not be suitable for your game but serves mostly the same purpose: licenses and certifications, giving benefits that open new opportunities for the player rather than making the character boringly stronger.
The character studies (spends time and skills points etc.), goes to the appropriate places for paperwork and examinations, and becomes able to acquire and use advanced equipment (from flying car driving licenses to fusion reactor operation), obtains legal privileges (e.g. investment as a privateer or permits for ship weapons), accesses nonpublic information (e.g. initiation into a guild or secret society) and so on. Stores, organizations, even ship computers can enforce such restrictions and make them important.

In some cases there can even be a challenging in-game test, involving a chance of failure and actual practice on the player's part.

Here is our progress on the skill tree.

Full size: http://atomictorch.com/Images/Upload/46.png

The tree itself is procedurally generated from a list of skills. Any skill can have a parent.

What do you think?

How does the player learn skills?

Make sure your skills and character progression are enslaved to your gameplay. Catalog the mechanics of the core game and build skills that impact that. As a long-time Eve player, I tend to think of spaceship skills as passive skills, leaving the selection of active abilities in the realm of ship loadout. Let's take a look at your skill tree ideas:

Piloting: This one's pretty easy, and can be paralleled to the Eve Spaceship Command and Navigation skill sets. A library of skill boosts would be appropriate here. Maneuverability, acceleration, top speed, inertial dampening, fuel efficiency, whatever influences your ability to fly the ship effectively will fit here. Ship-specific skills can deepen and expand the library, so you can have a skill that boosts top speed, then have another skill that further boosts top speed in fighters, allowing players to spend points both for general aptitude and for specialization.

Combat: Think about your forward-firing weapons. Do they have aim assist? Do they have a random spread? Give the player skills to improve rapid-fire accuracy or rate of fire or chances for critical hits or cooldown on special weapons. Player skill will let them point the ship at a target and pull the trigger, character skill will load the dice in their favor when the RNG takes a hand. Guided weapon systems like missiles and torpedoes could similarly be boosted in performance by the relevant skills, allowing a player to get really good at targeting and electronic warfare in a general sense, and then get extra good with masers and mass drivers as they level up and specialize.

Engineering: I'm thinking of this primarily as a defensive function, combining Eve's Engineering and Mechanic categories. Various stats like HP and HP regeneration and resistances could all be bundled up here. If your game features a mana/capacitor stat, that could fit here nicely.

Other: I don't like the idea of having a "Miscellaneous" category in a skill page. It seems clumsy and unpolished. If it doesn't fit into a category that's worth pursuing and building upon, then it's probably not worth having a skill for it. What would go here? Cargo capacity? Fuel Capacity? Communication range? Equipment hard point overrides? Funny hats? Shoehorn it into one of the other trees or move it to another system. Novelty effects could be equipped, maybe in an unobtrusive "utility slot" that can't be used for weapon or shield components. Boosts to non-core systems could be low-cost, optional branches in one of your three main trees. Don't let your players know that you have a "kitchen sink" category for shit you couldn't fit in or do without. That's weak.

Thinking further, a lot depends on whether or not you'll allow respecialization of your character skills. If you can't respec, then GameFAQs' "best build" will become the only way to play, and you may as well just have a linear "level up" progression. With respec, you can control the pace of upgrades and the timing of respecs, so players will have a certain amount of versatility and power, which will increase in potency in a linear way. They'll never have all the skills at their level, but they'll always have any of them, and experience will allow them to be narrowly effective at higher and higher levels as they get stronger.

As with Diablo II and Path of Exile and other games of that type, you will inevitably see the rise of "build archetypes", where the players will invest far more hours in your game than your testers humanly could, and they'll distill the most successful and efficacious combinations of skill unlocks in mind-blowingly short order. That's not a bad thing, per se, but you should account for it. Respec is a good way to accommodate this.

How does the player learn skills?

Hm. What do you mean? You just click on the skill and bam, you learned it :) But you need skill points that you get by earning levels.

Make sure your skills and character progression are enslaved to your gameplay. Catalog the mechanics of the core game and build skills that impact that.

Yes, that's exactly what we did. 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.

As a long-time Eve player, I tend to think of spaceship skills as passive skills, leaving the selection of active abilities in the realm of ship loadout.

Yup, that's my idea too. We have ship modules for "action" effects. And skills add passive stats or ability to use something.

Piloting: ... A library of skill boosts would be appropriate here. Maneuverability, acceleration, top speed, inertial dampening, fuel efficiency, whatever influences your ability to fly the ship effectively will fit here. Ship-specific skills can deepen and expand the library, so you can have a skill that boosts top speed, then have another skill that further boosts top speed in fighters, allowing players to spend points both for general aptitude and for specialization.

Exactly. That's what this skill tree is about. Plus we made three major branches: fast fighters ships, slow and heavy ships, and civilian ships.

Combat: [snip]

While I totally agree with you on everything, we faced a problem of organising all these skills in a coherent three with pathes for player to pursue. So far I am not happy with any of our attempts. But maybe later we can devise something.

Engineering: I'm thinking of this primarily as a defensive function, combining Eve's Engineering and Mechanic categories.

Yup, mostly this. Plus civilian stuff like asteroid mining and manufacturing.

Other: I don't like the idea of having a "Miscellaneous" category in a skill page. It seems clumsy and unpolished. If it doesn't fit into a category that's worth pursuing and building upon, then it's probably not worth having a skill for it.

I don't really like it either, but if we don't add it then a whole lot of interesting skills would have to be thrown out of the game. For example where do you put a social skills? There are quite a few of them, but not enough to create a separate category just for them. So, they are in the other. And there are a number of skills like that.

Boosts to non-core systems could be low-cost, optional branches in one of your three main trees. Don't let your players know that you have a "kitchen sink" category for shit you couldn't fit in or do without. That's weak.

Maybe you are right. I will think more on this. Maybe there is a better way to go about it.

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.

If you can't respec, then GameFAQs' "best build" will become the only way to play, and you may as well just have a linear "level up" progression.

To be honest I wouldn't worry about it too much. First of all what determines the most what you can do is you gear. Plus if someone wants to be a munchkin it's their decision :) But the way we are preparing these trees there won't be a single best build. Maybe several really good ones, but it is certainly not a deal breaker.

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

Say you want a "Fight Pilot" type character, you'd care less about fuel efficiency and turret tracking and more about forward-firing weapon systems, maneuverability and targeting. 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?

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.