Thanks for sharing your ideas about these issues. Looks like you're the pseudo-moderator for the time being

As I understand it, Shield Mitigation is the efficiency concerning the amount of damage that the shields block. Think of it like armor, but instead of an armor number, it's a percentage. If the shield mitigation were 100%, then the ship would be invincible. If the shield mitigation were 0%, the shields would do absolutely nothing - weapon fire would go straight to armor.
I've had cap ships against a bunch of smaller ships reach 50%+ on this, but it was too fast to see what was really happening. The base value seems to be 20%. I would be interested to see techs that boost the base value or the rate of increase from damage taken. Perhaps also some weapon types should be shield-piercing?
... realize that a few cap ships plus a dozen or so Kodiak Heavy Cruisers is almost undeniably better than the equivalent firepower in pure capships. The combined instantaneous firepower of the Kodiaks allows them to concentrate and down a single ship in a very short time; if you focus fire on the enemy's capital ships, you can win almost any battle with Kodiaks, and an Akkan for targeting support (throwing in some Gardas if they have fighters).
I didn't get a chance to test it because I had won the game already. I built each ship type to see what its abilities are; I think you are refering to its targeting ability, and I don't know exactly what it does (multiple bonuses when using multiple Kodiaks?).
A mix is usually effective: drop a few gauss cannons around the circumference of the build radius, spread over an arc between the phase-lines. Use the rest of your tac points on hangars, one phase inhibitor, and if you're advanced, a planetary shield.
I noticed the autoplacement feature puts them at the right angle (facing the phase line) but too far back (I think). They really need to be right at the entry point for maximum effect. I know bombers are a pain; I started adding Kols into my fleets just for their flak ability (don't know how good the flak frigate is yet). I lost several cap ships once to a massive cluster of frigates with bombers and I don't know which weapons on cap ships can even touch them (autocannon?). The phase inhibitor makes sense if you have a heavily defended node which is a major chokepoint, or as a delay mechanism in weaker nodes for you defensive fleets. I usually add 1-2 repair stations to assist in keeping the defense automated (mainly anti-pirate). The planetary shield, to my surprise, blocks damage with a 50-70% chance. I think it should just be an added shield to the planet, so you have to destroy it first or spend twice as long taking down the shield (preventing immediate damage to the planet). I think people want to see it working more directly in that way (base shield, 3000 pts. upgraded, 5000 pts).
The expected functionality is that you can queue things up as much as you like, even queuing the build of buildings for which tech is still under development -- but they won't go past 0% build progress until the tech is actually done. If you have seen evidence that this isn't true, make sure this hasn't been reported yet and if so, make a thread on it, maybe even attaching a highly-compressed savegame (http://www.7-zip.org)
It's very hard to tell why constructors are being stalled sometimes (given some of their bugs). I think it's easy to forget what's "waiting" on something else too, so maybe the planet has 25/15 because I queued 25 tac points after queuing planet upgrades. I also thought I was recieving instant tech upgrades, but I think the devs already thought it all out. I think I was just confused because it's an unusual setup.
Culturally flipped planets often have buggy constructor ships or include the old owner's buildings in their logistics; it becomes difficult to develop the new planet. Perhaps when this occurs, all buildings in the sector should also convert? Similar problem when a planet is taken during construction; can't get constructors to build when I take it back sometimes. Planets flipped still project the old culture.
I guess I like the idea that a node can only have one player's buildings in it. If taking a planet would also take all defenses/buildings, reset cultural lines, and restore planet infrastructure, then a surgical strike at the planet becomes a tactic, and planetary shields are more important also. However, the static defenses need to be more capable of protecting the planet (you shouldn't be able to "run past" them and take out the planet). The planet should have its own short-range defenses as a backup to take out frigates or maybe one cap ship before falling, that fire only when being bombarded.
Also note that the Insurgency technology (the top of the Combat tree) adds more intermittent "pirate" attacks. If your enemies research this, you'll get pirate attacked with zero bounty. Yes, you can collect your own bounty on a faction, IIRC. You could in Beta 1, for sure, and probably Beta 2 as well. AGREED 100% on the bounty notifications occurring too often. The AI gets a little hyper.
I think it spends too much on bounties that it could use for other purposes. I don't know if pirate strength is related to the amount of the bounty, but they seem to spawn at a star and find their way to targets. It's sort of like buying 3rd party attack ships for that target.
I'm pretty sure the ion cannon's upgrade on the Akkan just makes it last longer - it has the same disabling effect, range, recharge time, etc. Or does it have the same recharge time?... Something to check up on.
I think I was looking at that when I upgraded, and the recharge time was the same.
Planet culture is always displayed 0.0 or 0.1. I assume this is because the game's not finished yet. The culture clash between planets isn't really displayed in numbers anywhere, but I'm sure people would like to know what's going on.
I see enemy planets where my culture line has hit, but nothing ever happens; sometimes, my own planets stop projecting new lines. I would like to see it in the infopanel for both (even if my intel on the enemy planet isn't current, I should still know if it's about to flip).
Capital ships set to attack a specific target aren't getting close enough to use all weapons (or at least it seems that way). However, they do seem to attack targets within range while moving around (even multiple targets).
Weapons range should be the same for all basic weapons for a particular ship; that would eliminate any problems. I remember seeing beams and lazers on the same ship, thinking it was rather redundant. Weapon types need more differentiation. Is the autocannon a flak gun? There needs to be a specific siege weapon on the appropriate ships for clarity, not just "does 65 damage to planets" on the construction infocard.
Would like to see ship weapon/ability ranges somehow (A circle, or a semi-transparent filled circle maybe?).
Great idea. Since different weapons and abilities might have different ranges, how do you propose the player visually distinguish one circle from another? Should there just be one circle displayed, depending on which aspect you hover the mouse over in the battleship window (the translucent window showing the ship stats)? If so, we'd need a way to get that window to stay up when you move the mouse off the ship or its icon.
I think it's best to limit the viewed range to one ship first of all (or it gets messy in a hurry). Basic weapons range is the main thing for tactics, and is shown when the ship is selected (if the option is on, better make it optional, a button, or toggled by a hotkey). Special ability ranges should be shown when hovering over the ability icon, making it context-sensitive in a way (because you want to know particularly at that time).
I think the culture mechanic should work as follows: when another empire's line hits your planet, it begins a process of converting the planet (which is displayed transparently as a "cultural revolt xx%"). Multiple/stronger culture lines hitting will increase the speed of this effect. The incoming culture must be stronger than your culture at that location for this to occur (the conversion speed is the difference between yours and your opponent's).
Isn't the conversion process of the phase-lines the equivalent of this? You can visually monitor how close the enemy's culture is to threatening your planet, and e.g. demolish a logistics structure to counter their broadcast center with one of your own.
I would like to actually see it happening on the planet infocard. One potential problem is the fact that an asteroid can never broadcast as much as a planet (due to logistics limits). If they faceoff, the asteroid would lose unless it gets backup culture from planets behind it. I am curious how much culture is lost for each jump. The tug-of-war concept is intuitive, but it needs some work on the actual mechanic of it.
I think this is important: People want the option to use war or diplomacy. Here is one way: when planets are taken, all culture on its connected phase lines is lost. You can't change your capital planet (sorry, it didn't make sense to me anyway). The sum of all of your cultural sources is projected from your capital, losing a small value with each jump. This creates a "zone of control" around the capital, rather than local broadcasting spamming to take border worlds. Each planet produces a small amount of culture based on population, but the broadcasting center just provides a bonus "+xx%" for this. The effect of this new system is to make controlling the immediate area around the capital easy, while actually flipping enemies planets is hard unless your culture is much stronger or they are closer to your capital. For each jump closer to the enemy capital than yours, you would need for example 25% more culture than the last jump (it all depends on each player's culture though, and the rate of loss with each jump). If both have equal culture levels, then they would naturally control the same distance over time. If someone has 50% higher culture, they can perhaps flip one layer of planets closer to my capital, but not all of them. You get diminishing returns for higher culture because of the drop in effectiveness with distance. I hope that all makes sense, otherwise I will have to do it graphically.
Interface: add pip marks for buildings that are under construction (or make the icons faded).
Not sure what you mean here. Do you want to visually monitor construction progress of buildings in the sector? I am pretty sure this is already implemented, if you zoom in so that you can see the building's model. If it's iconified you may not be able to see the construction progress indicator.
I am zoomed out most of the time, so having the icons show construction will remind me that the planet I took a few minutes ago is NOT finished building defenses yet when there are pirates en route, for example.
The production/income penalty based on distance from the capital is probably too much and needs to be balanced. I think instead a better penalty is lower resistance to cultural takeover. An alternative is to make the maximum income penalty 30% or some other reasonable value, but I don't think it should reduce mineral mining rates in any case. Whatever it is should be a mild to moderate effect.
Two separate issues here. I think the income penalties are fine and probably play a large role in the balance of the game, concerning the amount of money that players get. As for lower resistance to cultural takeover, I think this would be a welcome change. Culture needs overall revision, and part of it would be to make it easier to take non-home planets, and exponentially harder to take planets closer to home.
As explained above, I think the cultural implications of distance from the capital are a more compelling game mechanic. The other penalties seem a bit harsh currently.
The refinery and trade post work as they are, but it's hard to see how much they are actually creating. I would prefer just seeing a boost to local mining/income for each building constructed (as a +xx% bonus). However, I'm sure it's a game mechanic that you want in there (maybe so they can be possibly destroyed en route). In any case, it's unclear whether the units are moving about efficiently or if there are too many; I'd like some more information in-game about what's going on, so I know about how many to build. One possible thing to do is have it giving a percentage of the bonus based on how many of its ships successfully completed runs (so when some die, you lose a part of the bonus, as intended); that makes its effect more measurable.
Put the mouse over the resource numbers indicating how much metal and crystal you have. This will display a list of the amount of resources in asteroids on your planets, as well as the current amount of resource currently in-transit by your refinery/trade ships. If you monitor this value over time, you can get a feel for how much resource is coming in - spec out the estimated trip time for one of your refinery ships, then you can figure that you get the average number of ferried resources per round trip time interval. Not the easiest to do, but I find myself calculating this in the background as the game goes on.
I still end up building them randomly with extra slots "just in case" I can get more out of it. I have no idea what the limitation is, but I think the trade center can be used more often (I can also buy the others with cash).