Ok, so there are some things that are either bugs, or ergonomics issues... or maybe it's me... 
1) Why sometimes rebel "white" vessels (that do not belong to any faction) arrive from nowhere and start attacking my planets ? That's not an allegiance issue as far as I can tell because my planet stats did not show anything wrong with allegiance when it occurred.
2) Why, when those rebel ships arrive, my Orkulus star bases look at them until they finish bombing my planet and everything around without moving at all ? The station is in its default attacking position which normally makes it guard the whole gravity well (thus chase any enemy getting in).
3) Why when I give a series of orders to my fleet, like for instance destroy the remaining structures on a planet, they seem to start doing what I asked, and after a (very short) while everyone goes where they want, drop bombs and lasers here and there but not at all on the targets I asked or in the order I wanted.
4) That is probably my bad knowledge of the game but, is there a tip to select all bombers or all fighters in the same gravity well (but not all of them together).
Thank you very much in advance for your replies.
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Summary of answers gathered so far:
1) Why sometimes rebel "white" vessels (that do not belong to any faction) arrive from nowhere and start attacking my planets ? That's not an allegiance issue as far as I can tell because my planet stats did not show anything wrong with allegiance when it occurred.
=>This is a TEC tier 8 tech that causes militia to randonly attack enemy planets. You'll need to leave some basic defenses, though the one starbase will be enough.
2) Why, when those rebel ships arrive, my Orkulus star bases look at them until they finish bombing my planet and everything around without moving at all ? The station engagement range was set to whole gravity and auto attack feature was on too (I guess it is default).
=> Bug
3) Why when I give a series of orders to my fleet, like for instance destroy the remaining structures on a planet, they seem to start doing what I asked, and after a (very short) while everyone goes where they want, drop bombs and lasers here and there but not at all on the targets I asked or in the order I wanted.
=> Its possible if they were hit by certain abilities that effect movement or disable ships their orders were reset. Things like the Advent starbases mass disorientation, repulse, or ion bolt could do that. Also if you're attacking another Vasari gravity well they have an ability to phase out briefly, which is annoying as it also resets you orders, or at least skip that target.
4) That is probably my bad knowledge of the game but, is there a tip to select all bombers or all fighters in the same gravity well (but not all of them together).
=> If you hold down alt when clicking a unit it selects all units of that type in the well not already selected. This actually works for anything. Ships, structures, etc. You can also click either on the object directly or from the side bar.
Complementary info: The little side bar that appears at the edge of a planet with ships in the grav well.
Click it once to select all combat ships.
Click it again, and it will select the non combat ships like colony frigates.
Click it a third time and it will select all strike craft.
5) At a certain point, I couldn't send more pirate regular raids against some enemies (there was a sort of pirate saber in front of their icon). I believed it was because they were already under a pirate attack but it lasted hours... In middle game, almost half or the 12 players had that symbol.
=> Confirmed: a sword near a player in the pirate menu means a raid is being done on the player. So on the game I was playing, someone was probably being raid all the time... I will check if pirate missions generate the sword icon also.
Complementary information:
To answer this, one of the TEC factions (I forget which) has a research upgrade that allows them to ally themselves with the pirate faction, as well as any other rogue (white) fleets. If the enemies immune to pirate raids are TEC, this should be why.
6) I noticed a symbol indicating the presence of an artifact on a planet. Is that symbol automatically displayed or is there any prerequistite in the restearch tree for instance ?
=> The artifact indicator only shows on a planet after someone has searched and found an artifact. In other words, you'll see the icon on enemy planets once they have the artifact. It will never show up on your planet unless you explore the planet, even if there's an artifact there - unless you took the planet from an opponent, obviously.
7) There are other benefits that are not artifacts on planets. If I understand correctly:
- Artifacts may be displayed with a symbol while advantages may not
- Artifacts apply to the whole empire while advantages apply to the gravity well
=> Correct
8) There are orbital structures like trade ports, matter processor that work with planets around. However, I couldn't find the way their income is calculated. My guess is that trade ports have a higher credit income if the nearby planets have a high credit income. Matter processor works the same but based on the number/rate of exploitation of asteroids in adjacent gravity wells ? Is there a rule available to know whether it is worth building such structure or not ?
=> Details on trade ports: https://www.sinsofasolarempire.wikia.com/wiki/Trade_Port and https://forums.sinsofasolarempire.com/423345
=> Details on orbital refineries:
"Refineries can exploit owned and adjacent resource asteroids. Asteroids can only support so many refineries at a time though."
WILL DOUBLE CHECK THE REFINERIES PART IN MY NEXT GAME
9) When an alert is displayed (ex: planet xx is under attack) I'm quite sure there is a shortcut to go there directly in one click but I cannot find it.
=> You can press on the warning than press space.
10) What is the purpose of the fleet feature ? Here is what I understood :
- Have your new ships auto assigned to a fleet
- Have your ships stay close to the leader (could be interesting if for instance you want your flak force close to your planetary bombardment ships to prevent strike craft)
- Have your fleet gather once they have accomplished individual orders
Besides the "guardian" idea, I really wonder it it's worth spending time creating them.
=> STILL OPEN TO DEBATE. More cons than pros so far.
11) How do you select the fleet leader ? If all the ships are the same, it does not count much but if not, I may prefer selecting capital ship A than B as a leader. It seems the game selects it for me among the members of the fleet.
=> The fleet leader should be the ship you actually have active when you press "create fleet." I feel like I've seen this glitch before, though.
Press TAB repeatedly to switch to the ship you want to be the leader, then reform fleet.
12) Tight vs loose formation:
I believe the interest is to adapt the enemy situation.
- Avoid splash damage with loose formation
- Pass through a small gap in a minefield with tight formation
But I have not seen any difference with the placement of my ships.
=> PENDING
13) Is the penalty different when you reject a mission and when the timer expires ? My guess would be it should be lower (otherwise what is the point of having a reject button) but I couldn't find what is the difference exactly.
=> Rejecting a mission does indeed incur a lower penalty than failing one.
WILL CHECK PENALTY DIFFERENCE IN MY NEXT GAME
14) It is weird that sometimes, another AI player had a good opinion on me but according to the game I didn't had a good opinion on him (ex: I was 6 to him but he was 2 to me). I had somehow to send him fake missions to higher my opinion on him and make pacts. Is there any other mean to do this because this part is a little boring ?
=> The best mission you can give another player that you want to ally with is "Send Envoy." You'll get the boost from the mission completion and a continuous one from the envoy being around. Also, the AI tends to all-in with envoys, so there'll be on around each of your planet. As a bonus, envoys boost the effectiveness of a planet.
STILL DIGGING THAT TOPIC
15) What is the cooldown when breaking a peace treaty before you can attack your former partner ? "After breaking a peace treaty, neither nation will be able to attack the other for some time."
=> 1'30'' maybe 3' to be checked (somewhere around this
)
Complementary info : cease fire can be broken without delay.
16) "Once a Pact is formed, the bonus it yields applies to both parties. You may only assign each of your Pacts to one other player; Pact bonuses will not stack in cases where you may be offered the same Pact from two players of the same race."
I believe my own bonus does not stack either, even if the 2 partners are of different races ?
=> I'm fairly certain that you cannot make the same pact with 2 different factions. This negates the possibility of stacking pact bonuses.
TO BE CHECKED IN MY NEXT GAME: I'll try to see if the situation occurs in my next game. But it seems weird they mention a case that does not exist in the rules.
17) Fleet logistics => I'm pretty sure there is no rollback possible to reduce your upkeep. Can you confirm ?
=> No rollback possible. As soon as you get a fleet logistics upgrade, it's permanent. So be careful when getting those upgrades, otherwise you might end up killing your economy.
18) Is there a way to guess which planet is to be the target of the pirates ?
=> There's no way to know a priori which planet will be targeted by the pirates. Just scout / monitor phase lanes like you would for any attack. Usually, they will go for the nearest and weakest planet, but I'm not sure of the exact logic.
19) Kostura Cannon:
If I understand well, it disables structures for 3 minutes without damaging anything, does not even disable starbases, does not stun ships (making it more an economical weapon it seems). Is it worth the price ? How can you use it effectively ?
=> Kostrua cannon disables all structures, including starbases. However, what makes it powerful, is that it makes the targeted planet a phase stabilizer node.
This means you can jump directly to the target, allowing you to hit the soft underside of enemy empires rather than going through the front lines. Especially nice to get the K.O. on capital victories. A pair of Vulkoras Desolators, an evacuator with drain planet, and if needed a small group of siege frigates can make short work of it. Just note the node is temporary, so you'll need a Marauders' ultimate ability, a starbase with the phase gate upgrade, or after you conquer and colonize the planet a phase gate structure to get back.
20) About shield Mitigation: I understand that the more you shoot at a ship, the more percentage of damage is negated.
So basically what is the best way to take down an enemy fleet ? Focus fire on each enemy shipe one after another or alternate on a group for mitigation to drop ? Personally I focus fire but maybe it's just nonsense...
=> STILL OPEN TO DEBATE: More focus fire than switching targets so far