Generally, in Starsector you can do good picking whatever skills you feel best suits your playstyle. Combat tree (With a bit of technology tree) is good if you want to be the combat hero like in Mount & Blade. Leadership is better if you prefer carriers and to buff your fleet by adding more officers, increasing CR, etc. Technology is a combination of personal combat skills, fleetwide buffs, and campaign skills, and industry is for making money especially with the new colonies.
1. Do sensor jammers and nav buoys appear in battle if you don't have their skills and what exactly "up to a maximum of 10% without skills" mean?
They'll always appear once the total DP of the ships involved are greater than a certain value. The maximum statement means that without upgrading those skills or Command and Control to level 3, then you'll always max out at 10% speed no matter how many nav buoys you capture/ships you have in your fleet and same with Sensor buoys and enemy range.
2. Level 3 Command & Control applies to level 1 Coordinated Maneuvers and Electronic Warfare?
Yes, it should also apply to unskilled Coordinated Maneuvers and Electronic Warfare as well, but really it's not too important aside from min/max building to outrange stations with Paragons.
3. Level 2 Command & Control 50% bonus is worth it?
Depends, Level 2 Command & Control (and the Operations Center HullMod) are designed to allow you to take a more commanding role in battle rather than directly fighting. HULMUT had a post in general back in 0.8 about doing a pure commanding run where he used a Hound with Ops Center to great effect to command a fleet of Odysseys and Astrals.
4. How Loadout Design actually fares against the late game?
90% of the time, you'll find that people will take Level 3 Loadout Design. Levels 1 and 2 are a bit lackluster but level 3 is where all the good bonus comes from. This is due to the fact that its very versatile in its use in how you build the ships in your fleet and can make ships that feel on the fence much stronger by allowing them the vents or hullmods they need to become really strong. Loadout design is pretty good early and late.
5. Is -25% supply usage and +15% combat readiness from Fleet Logistics impactful, or you can always circle around both with, for example,Efficiency Overhaul?
As mentioned above, Combat Readiness(CR) above 70% begins to gives minor general buffs to ships and inversely for ships below 50% CR. You can circle around the supply use/fuel use reductions with Efficiency Overhaul since its very cheap and the enemies while exploring aren't too tough. Though the Skills for reducing supply/fuel usage are very useful when exploring long term or distances and can be stacked with efficiency Overhaul. Also, this is a good example of how Loadout design 3 can be good, if you instead go without the supply skills and go with Efficiency overhaul, the 10% OP will cover the cost of the hullmod since its so cheap effectively replacing itself with the reduced usage skills.
6. Does Fighter Doctrine stack with Officers skills?
Yes, it will stack with officers and your own skills. Usually if you dabble into leadership and have carriers in your fleet you'll want to get fighter doctrine since it and carrier command give the best buffs to fighters.
7. If level 3 Officer Management, Combat endurance would be a better pick than Fleet Logistics?
Fleet Logistics will stack with Combat Endurance giving a max CR of 100%. 100% CR means 10% Damage dealt, maneuverability, speed, and reduce fighter refit time and damage taken by 10%. So if you want to, you can get both. Before 0.9 colonies I would get Combat 3 only for Combat Readiness, but now I'm thinking of getting Combat readiness 1 for 2 points since its too large a commitment in tandem with new colony skills.
Edit: Forgot to mention this, but Fleet Logistics 1 pairs well with Officer Management since it means that you'll always be able to recover any ships with officers in them so you don't need reinforced bulkheads for anything you want to keep but can't easily replace.
8. Navigation skill worth anything?
Up to your decision, the fuel use reduction is great for going out to the fringe and exploring, but if you're getting Nav 3 its really for the Transverse Jump. Transverse Jump has the campaign utility of jumping in close to any planet in a system and jumping out from anywhere, bypassing typically fortified inner jump points and avoiding long detours of outer/fringe jump points. When combined with Sensors 2, you can jump in and do almost anything stealthily extremely easily unless you happen to warp directly on top of someone.
Below is a post I made before about my opinions on each of the skills if you want to read about them.
Spoiler
Combat:- Combat Endurance is actually a pretty nice skill to get assuming you decide to put points into combat tree. Level 3 stacks with Fleet Logistics 3 and can give your (officers') ship additional combat bonuses from higher CR. Also having extra PPT for lasting power is very nice in general and even necessary for smaller destroyers and frigates. That said its a skill generally only gotten with 1 or 3 points.
- Missile spec can be absolutely devastating if you want to live in a Gryphon cruiser or Harbinger for the rest of your life in SS. Otherwise, it might be useful as a backline carrier but there are other things you can spend points on.
- Between Ordnance Expertise and Target Analysis I believe Target Analysis does a bit better at taking down enemy armor, but of course it loses out at hitting the hull aside from knocking out enemy weapons/engines better. Can pair well with Ion though at level 1. Naturally, Ordnance Expertise 1 has a bit better effective DPS due to missing less shots on faster targets.
- Damage Control's best level is actually level 2 for the faster turn around time with engine/gun repairs. No matter how good you are you'll have to contend with Ion and the only non-skill reducer to that is Resistant Flux Conduits(hullmod, RFC). Having a fast turnaround time on your engines/weapons means you're less concerned with them getting knocked out and if you have the OP to fit Automated repair unit(hullmod, ARU) allows you to just about ignore it.
- IIRC Impact Mitigation is currently borked and instead of increasing armor values linearly, it increases armor by 150% on level 1 right now, though Alex has stated that its fixed for next patch. The short answer though is that armor works exponentially so even if it was a flat 150 it works much better for heavier ships, but a flat 150 would be good for frigates too. Here's a handy link for more in-depth look into armor here!
- Defensive Systems is generally good, but it needs to be cautious about level 3. While faster phase cloak can be useful, most of the phase ships don't need it and ultimately it gives less lasting power.
- With proper shield use Advanced Countermeasures can actually provide better shield buffs than defensive systems. I believe Thaago had also described a good use for them, by putting them on some of your officers you can effectively shutdown enemy fighter/missile superiority even with mostly warships.
- Level 1 of Evasive Action is generally the most popular one, but its level 3 armor perk is pretty good only falling a bit behind Impact Mitigation for effectiveness and pairs very strongly with it.
- Helmsmanship isn't nearly as good to max out as it used to be in 0.7. Now that carriers no longer abuse it with their fighters (It automatically raises flux above 5% to engage with fighters.) 5% flux is really only good to run around with 0-flux boost with your shield up w/o taking damage and firing only token low flux PD.
Leadership:- Command & Control is there if you want to play SS like a RTS game really. There's a quite number of people that prefer to autopilot their flagship, but in actuality HULMUT discovered that it was better to slam OPS center onto a hound, sit in the corner and command from a far. Generally pairs well with Officer management.
- Officer Management can be really good depending on your fleet preference and your max battle size. 6 extra officers technically means 42 extra skill points in your fleet as well as 6 ships with a different behaviour then your assigned fleet doctrine.
- Fleet Logistics really is overtuned right now IMO. lower supply costs, nearly guaranteed ship recovery for officered and your own ship, and CR on top of colony Accessibility bonuses easily makes this one of the best skills in-game with the honor of all levels being very useful on its own.
- Coordinated Maneuvers is very good to get for level 1 so that you're just about guaranteed the bonus 10% depending on deployments and lets you completely ignore the nav objectives in combat. That said the higher levels have diminishing rewards with only 5% max raise so they're only good if you're using faster ships. Though it should be stated that unlike Electronic warfare, the extra levels are independent of the enemy and always useful based on deployment.
- Fighter Doctrine is generally always good if you plan on using carriers in your fleet. Not only does it provide vital fighter replacement rate help, it will also guarantee you expanded deck crew at level 3 which is the Integrated Targeting Unit(hullmod, ITU) of dedicated carriers.
- Carrier Command and Wing/Strike Commander are carrier skills. If you plan on commanding a carrier then these are vital to fighter performance.
- Planetary Operations can be take it or leave it. Additionally the +2 stability can be an extra colony if you desire, since being above/below the administration limit means a 2 stability penalty/bonus for each count to the limit.
Technology:- Gunnery Implants is very good if you plan on piloting gunships. +range is always very useful and the weapon recoil helps a lot with weapons that have poor accuracy like the mortars. The autofire is mostly useful for hitting missiles, fighters, and fast frigates.
- Power Grid Modulation is also very good if you plan on piloting gunships but not necessary if you want to pilot carriers. That said you can either go for level 2 or 3 IMO. More flux dissipation is nice, but the level 2 I feel is the best bonus as it means you active vent much faster lowering your vulnerability window.
- Electronic Warfare is extremely useful at level 1. Without level 1 you can suffer up to 20% range penalty depending on the enemy while with it you can protect your range or nerf the enemy's range by 10%. Higher levels are not so useful do to it being compared against the enemy's ECM stat so if they have EW1 its unlikely that you'd get the full bonus and if you do then you severely outmatched them anyway. That said, enemy's rarely have this skill aside from the high tech Tri-tach and maybe Perean League?
- Loadout Design is considered one of the best explicitly for its level 3 perk for giving more OP for ships. Otherwise, its not so good as you need OP to take advantage of its level 1 and 2 perks.
- Sensors feels like a bit of a convenience skill for the sensor game. Neutrino detector can help with finding objects not near celestial objects. Meanwhile I'd say level 2 is the only really neccessary level for this if you choose to get it. Now with Logistical hullmods its possible to keep your profile lower and level 2 will help keep your sensor higher than your profile and give you the added bonus of a mobile asteroid field cover with "Go Dark" ability. Level 3's movement during active sensors doesn't seem as useful.
- Navigation's level 2 is good for fuel conservation, but drams and phaetons carry more than enough fuel anyway. Personally, while +1/2 burn speed is nice I believe that Transverse Jump is the best part about level 3 as it allows you to completely bypass the jump gates. Very good for sneaking into enemy territory as well as saving time (and occasionally supplies).
Industry: I can't be very descriptive with this one since I never used much of it in 0.8, but its good for a fleet of makeshift junk. Its claim to fame in 0.9 are the colony skills.
- Safety Procedures is good for going through hyperspace storms and saving up supplies at level 2. Can also let you spam E-burn like AI did in 0.7 and 0.8. Wyvern added that you're also able to use E-burn with mothballed ships, which you're not normally able to do giving you some flexibility.
- Recovery Operations seems like it'd be good for gathering weapons, ships, and fighters early on but could fall behind in the end once you have colonies running and a fair stash of blueprints. Still it could nab you that specific thing you don't have a blueprint for.
- Field Repairs is good for saving supplies in the long run with a fleet of clunkers, but since its level 3 skill applies to D-mod ships it loses its luster once you start producing/restoring your own pristine ships. Also I believe that its faster ship repairs applies specifically to hull/armor damage and not CR which is typically the bottleneck with post-combat recovery.
- Salvaging is good for getting the rare things for the colonies. I would recommend not using up any orbital habitats/mining/research stations and just noting where they are if you plan to max this out. Also, when salvaging from those locations, salvage the debris fields too until there's absolutely nothing left. Its possible you might salvage the field 6 or 7 times before being sure of nothing more coming out of it.
- Colony Management is a colony skill. Good if you want more colonies or you want more stability for your fewer colonies.
- Industrial Planning is a definitely good skill if you want to go in on colony skills. Maxing it out helps increase your colonies market share while importing less if necessary (Though that just means less potential of losing output currently). The last skill of course just prints a hefty 30% colony income for you.