For current ToR empire the hierachy is; Emperor at the top, Dark council below them and then all the rest below various members of the Dark council depending on what their position is, the exception to this is Grand Moffs who are granted that position and power by the Emperor and have as much power and athority as the Emperor choses to give them, there are a few other exceptions such as the Imperial guard and Emperor's Wrath who are under the direct command of the Emperor and as such the Dark Council has no athorilty over them. For Palpatine's Empire it was a bit diffrent since there was only him and Vader with no Dark Council but as it stands Tarkin as a Grand Moff was not answerable to Vader only the Emperor and had likely been given fully athourity over the Death Star but could probaly not have ordered Vader to do anything when he was not on the Death Star unless the Emperor said so. As for the Grand Admirals they were never fully intergrated into the empires chain of command (the process was still under way at the time of Battle of Endor) but most likely the order of command would have been; Emperor-Vader-Grand Moff-Grand Admiral as the empire had its military subordinat to the civilian goverment with Vader being able to give orders to a Grand Moff or Admiral unless they went against the Emperor's instructions or the Emperor had given them the athourity otherwise.

This has been an issue with Biowears companion system since Kotor, everyone else is apparently incapable of doing anything without you, the only time in the Knights story you send them all off to cause distractions for you and even then you have to go save one of them (or not, you get one of thoses LS/DS choices that means nothing, and it does mean nothing they survive no matter what). They really need to make it seem like the companions not with you are doing somthing other than sitting around the ship when you are getting shot at, blown up, electracuted, stabbed and other unplesent things.

All I will say about your second spoiler is:

To the first part yes I meant Andronikos, I have got to stop making post when half asleep. As to the view on how much detial the canon versions of the story lines should have I would agree that the detial should be very limited, after all the Kotor 1 cannon (by that I mean the game only) is no more detialed than; Male Reven, Light side and married to Basitila. As to the Sith warrior, I understand that when you make Jessa dark side she really goes off the deep end with it and I think that the limitations of the game design should be ignored when writing the SW canon line and that Jessa should be turned down to be Dark gray alinmant like the warrior, the main reason for going with that alinmant are: Too dark means a vegtable Miss... sorry Vetta and again there is no way you could argue that Quinn was kept alive after that "incident" with a full dark Sith (unless you want to ignore the game here and kill him off), and a light side sith serving as the Emperors personal Exacutioner and enforecer of will is a bit off. As to a female JK, I didn't go with this for two reason: 1. I hate Doc 2. I think a male with a Kira romance makes for much more in the way of story possibilitys.

Well its unlikely that Palpatine only had one way in and out of his personal room on the Death Star, there was likely another way out behind the lift (he did have a hidden passage system built in along side the lifts he added to the impirial palace on corasunt I would think he did the same with the death star), as to why the guards did not come back I would say they had been told in advance that Luke and Vader would end up in a fight and not to interfear and that he had also sealed the room to prevent Luke just running for it.

So eventualy there will end up being canon versions of the class storys, so what do you think they will be? Personly for the JK, JC, SW and SI I think it will be the following: Jedi Knight: Male, Light side (like it was ever going to be dark), married to Kira (not officaly but Satile probably finds out, possiably the rest of the council as well). Jedi Concular: Female, Light- a shining exsample of what a jedi should be, no romantic relasionship, ends up on the jedi council (if they did not already, bit weak on their story). Sith Warrior: Male (the main reason I am going with this is Quinns betraly happens no matter what and it would be a bit silly for that to happen if it was a female sw who could then marry him), Gray/dark- dark but not the kind of sadisticly evil sith we have a lot of, married to a Dark side Jessa. Sith Inquisitor: Female, Dark as dark can be (lets the unwilling ghosts go though as it looks to be the wiser of the options), kills off Thantons followers at the end, has a relasionship with Andronikos but its more "attending to her physical wants" rather than any sort of romance, puts down a couple of attempts to un-seat her from the council. I have done these more as a vague overview as there are so many options I don't even want to guess at I felt it more suited.

Well since they make a point of saying that all the jedi survived the fights in the run you have discribed I would guess that She may end up getting killed or injured if she fought, this would also ofcourse "annoy" (to put it mildly) Kira quite a bit. As for the non-generic npc's you get (i.e. the ones you had to fight and could have killed) I would imagin that you just get Generic Knight number 6752 in there place but they may have of characters you couldn't have killed for thoses spots.

And how volitial would the power generators of such a ship be if the went bang? Well at the top end of the scale the reactors on both Death stars going critical was a large enough exsplosion to destroy somthing the size of a small Moon. Therefore on a standered warship its reactor going critical would like blow it in several large bits and best. Also as to the theory of only a part crashed on the surfece (and from the quests a part with sensor records and at least partly intact data systems) how did it survive; uncontrloed re-entry, crashing into a city, orbital bombardment (to quote Carth "There was not a building over two stories tall left standing") and 300 years of ratghouls and uncontroled natrual ecosystem reassertion? And is it just me or do the republic cruisers of 300 years ago look a lot like the republics current frigets?

Given that I saw the thing get consumed in a gaint fireball is KotOR I would like to now how it is relitivly intact on the surfece of a city planet that was on the reciving end of heavy orbital bombardment 300 years later.

Ok first point, in Star Wars as in reality using stratigic level weapons on planets that you want to control is not a good idea as you could not then use the planet, in space is another matter. Second to control a planet you must have ground forces on that planet, if you wish to take that planet from the enemy you must remove their ground forces, hence land battles (and don't say take them out from orbit as that would casue a lot of damage to the planet you are trying to capture). Third the relitive strength of Jedi/Sith declining could be due to the fact there are less of them to teach the new ones, and lot of the knowlage is lost, if you have to spend most of you life just learning it yourself you do not have much time to advance it after you have finish learning where as if you are taught it in a fraction of the time you can contribute much more.

Well he did turn up again on Correlia and I would prefer him to that insufrable Scourge and that would have some intresting drama potential with Kira.

Oi leave the droid alone he's one of the two companions I have who I don't feel like using for saber practice. As for the main topic why do the sith get some corruptable companions but the jedi don't get any redemable ones, hell as the Jk you get stuck with a 300 year old pure blood sith who may be responsable for this whole mess in the first place.

"No fuel as such" Yes they require Ionised partical to accelerate but space is not empty and is filled with said particals that can be drawn in to provide that fuel, and yes ship would likely have a "reserve" store if for use if they need a quick increase in the speed or have few particals to take in.