How would you guys handle this in terms of choosing the skills:

The PCs have snuck onto an enemy ship. They seal themselves up in a cabin in order to slice into the ship's computer system unseen. One guy stands with his ear to the door, listening for the sound of approaching enemies.

Would the character on guard at the door make a Perception check to hear someone coming down the hall? Or would you say Vigilance is more applicable in that situation?

I agree with those who've said Perception. Since the PC has actively chosen to listen at the door, I'd say Perception covers it.

If the PCs were in the room and you wanted to give them a chance to overhear somebody listening in from outside their door, or someone sneaking up on them, I'd rule that was Vigilance myself.

Vigilance could be also described as "paranoia." Being vigilant in this sense doesn't necessarily mean you're good at noticing things, but rather that you are good at dealing with the unexpected.

For those that suggest combining Cool & Discipline, you've also got to consider that Discipline is the "Force power" skill. Throw in the fact that Cool is used for things like ambushes, regaining strain after an encounter, and doing a good job of keeping a cool exterior, Discipline would become an overpowered "must-have" skill. Game balance is as much a consideration as any, and the two skills DO have enough difference that their separate existence is warranted. I know some feel differently, but IMO the deletion of any skills from the core game only serves to unbalance things and take away from the Star Wars-y feel. I think the devs got it right with the skills, and messing with them just creates more headaches to deal with.

I've diferentiated the two as perception is noticing something that is there but not obvious whereas vigilance is more noticing a change in the situation. With vigilance, you probably don't see it before hand, but you do notice it in time to react.

For example, with perception you notice the small hole in the wall and can react before the dart whereas with vigilance you can react as you hear the click and react.

Perception, you notice the small blood stain on the ceiling. Vigilance, you spot a drop as it falls to the floor.

Perception, you notice the thug crouched in the shadows ready to attack. Vigilance, as the thug springs forth you react and are not surprised.

For those that suggest combining Cool & Discipline, you've also got to consider that Discipline is the "Force power" skill. Throw in the fact that Cool is used for things like ambushes, regaining strain after an encounter, and doing a good job of keeping a cool exterior, Discipline would become an overpowered "must-have" skill.

Regaining Strain is already a Cool or Discipline check, so that one can be discounted.

I never understood how if you are aware of an ambush or an attack on the way, you would think that you would have time to prepare and get a higher initiative slot. But if you have no ranks in Cool and a crappy Presence, then no matter how much warning you have, chances are that you will make a slot later in the combat. Whereas someone who doesn't know it's coming but has a high Vigilance will probably open an early-round slot.

Has anyone seen any kind of reasoning behind this that makes sense?

It's possible to be quick at reacting but not as good at planning things out.

Maybe purchase ranks in Cool to balance this out if your character's meant to be Cool under pressure.

Or handle it however you think makes sense for your own game.

I'm about to go slightly off topic and also full frontal nerd-ity on everyone, so bear with me.

About twice a year I take part in a LARP set in a post apocalyptic earth. In one scenario, the players were crowded around some thugs holding 2 of their leader's hostage. There was no point in vigilance. Everyone knew that combat was about to break out so if this were a edge game, it would be cool checks. Tensions were running high, and everyone had an itchy trigger finger - we play with nerf guns.

One of the thugs misread the situation and open fired too soon. Again, were this an edge game I would have called for initiative checks using cool at this point.

Those that kept cool, quickly moved to cover or began to assess threats. One player did not remain cool, he was hoping to end the fight quickly. He ran up and exposed himself to gun fire, and threw a grenade into the throng of enemies.... and hostages.

Anytime I want to explain to my players the distinction between cool and vigilance, I throw out that story.

I never understood how if you are aware of an ambush or an attack on the way, you would think that you would have time to prepare and get a higher initiative slot. But if you have no ranks in Cool and a crappy Presence, then no matter how much warning you have, chances are that you will make a slot later in the combat. Whereas someone who doesn't know it's coming but has a high Vigilance will probably open an early-round slot.

Has anyone seen any kind of reasoning behind this that makes sense?

Some people, the more they think about something, get more and more indecisive and will often just... "shut down" from the stress.

One of the thugs misread the situation and open fired too soon. Again, were this an edge game I would have called for initiative checks using cool at this point.

It seems to me because this thug changed the situation, it would have called for initiative checks using vigilance. Or maybe it depends on how you'd want the twitchy thug to play out, does he get to fire first or not?

Vigilance: "Uh oh, somebody is about to lose it. Shoot first!"

Cool: "Dang, that guy lost it and is already shooting up the place. But I can get behind those crates before he can fire again."

From my point of view, it's about the "value" of the skills. As I have a relatively combat heavy (action heavy if you want to say it nicely) game, vigilance is a valuable skill simply because it determines initiative in 95% of the situations my players find themselves in. Perception is also valuable as it helps spot stuff... important in any RPG.

So if I added in a lot of passive perception checks to vigilance, it would rapidly become the must-have skill over perception for my players. The exception to this would be when a character needs to be attentive to his surroundings over a loooong period of time, guard duty being a classic example. Then I would ask for a vigilance check to notice the bad-guys trying to sneak up on the parties ship with a crate of baradium charges. Actually, I would probably roll the bad-guys stealth with difficulty being set by the characters vigilance.