As far as I know, once a mini has been set, it cannot be changed, and the first person to write a mission in that continuum is the one to set it.

I would still charge a Sue with being insubordinate, because even though Jack, in particular, gets away with insubordination, the rest of the personnel on the base does not. Daniel is mouthy all the time, but he is not military. Carter is not nearly as mouthy as Jack to higher ranks. I would consider a Sue getting away with it as an indicator of sheshulness.

I'm more familiar with SGA than with SG-1, having only seen the odd episode of the latter. Haven't noticed much insubordination, but that's probably because the military presence in SGA is less strong: in the first three seasons only one main character was military. He usually ended up having arguments with people who were not subordinate to him in the first place, and therefor could not be insubordinate.

Sues that claimed to have a military background (along with their scientific background, as do the characters from SG, but not the characters from SGA) were charged with insubordinace when they were. For instance, when showing up late for a meeting because of a bet or when a captain argued with Shepard that he gave her a small gun when giving everyone else a P90. Other military characters (or scientists for that matter) wouldn't have gotten away with that kind of behaviour, and thus neither should the Sue.

That's what we do: point out that the Sue is getting away with behaviour that the characters would not let others get away with.

As for fixing things that are wrong on the show: it has annoyed me to no end that Carson Beckett had a Scottish flag on his sleeve, while all the other personnel from the UK had the union flag on their sleeve. When my agents first did a mission in SGA I drew attention to that point by giving one of my agents the flag of England on her sleeve and have her argue against that.

Additionally, are you new? I don't think I've seen any posts from you before this.

1. Your agent is an arachnophobe, and you're even thinking of not taking advantage of the possible hilarity?! No! Don't change the mini! Of course, your agent doesn't have to adopt one, nor do you have to describe the mini anywhere past "a Mini-Aragog", nor do you even have to state that a mini has been generated... but this is potentially a cool thing. Your agent has to face her fears--does she turn into a little quivering ball, does she get violent and take it out on the badfic, does she hide behind her partner, does she eventually figure out that, "Yeah, I hate the creepy little things, but there are worse things in the world"? You have an opportunity for character development here. Don't waste it! (Also don't magically cure the phobia the first time she sees a mini-Aragog. That's just cheap.)
   
   2. Each continuum has its own rules. If insubordination is relatively normal in that continuum, it's not a charge. Similarly, having unusually colored hair in many anime continua wouldn't be a Sue trait, because so many characters do. But if it's over-the-top for the Sue's position or the situation, it can still be a charge.
   
   3. I hadn't thought of that. The way we have it now with quarantined continua, the characters from the quarantined continuum could only be character replacements, because the author can't access the true version of the quarantined continuum; so in this case it's not really an Implausible Crossovers fic at all. The idea of quarantine is there because we need an "excuse" not to PPC stories set in banned worlds (i.e., the author has banned all fanfic, so his continuum doesn't need protection). I would say that, to preserve that reasoning, the best way to resolve it would probably be, "When a fanfic author attempts to access a quarantined continuum for any reason, he is blocked and must create his own continuum. All characters within this continuum are essentially original characters, though heavily plagiarized."