Perfect Dark/Headscratchers

I get why Daniel would want Joanna to break into Area 51 to rescue Elvis, but in the meantime, why couldn't he have sent someone else to warn the president that Trent was trying to kidnap him? Are Joanna and Jonathan the only two agents in the institute?
- Maybe they're the only agents qualified enough or the only ones available.
If we are to accept everything in both console games as canon, then since joining the Institute, Joanna has adoped an english accent, been labeled "inexperienced" (despite the fact she used to be a bounty hunter and defeated a "god") and forgotten what Jonathan looks like.
- And Carrington has decided to ditch the kilt.
  - Well he doesn't ever look comfortable in that suit, does he?
- I can agree with you on everything but Johnathan. From the cutscene in Perfect Dark in which you meet him, it seems more like they do know each other, it's just that Joanna was still in "shoot everything that exists" mode, and Johnathan startled her.
  - No, in the original game, she comes upon a mook that she clearly thinks is Johnathan before Johnathan reveals himself.
    - Undercover agents can be wearing all kinds of disguises.

It bugs me that the RCP-120 can hold 120 bullets in what doesn't appear to be a very big clip. Still an awesome gun though.
- If you can accept a gun that uses mineral bullets which it converts into a light-bending cloaking device, then frankly that's the least of your worries.
I can understand that the Skedar are using holographic generators to make themselves appear to be a human under the name of Mr. Blond... but what I don't understand is how in the G5 building mission, Mr. Blond was sitting down in a chair, when a Skedar Warrior would be incapable of sitting in the chair.
- What bugs me more is that, if I recall correctly, they stay in their Blonde disguises when you kill them in the Crash Site mission. Avoiding spoilers, sure, but unless their disguises aren't lifeforce dependent ...
- It bugs me that his name is spelled "Blonde". It's clearly an alias, but they could at least spell it correctly, considering he's (supposed to be) a man.
- I guess to the Skedar, all humans are the same, so why would they concern themselves with something as "trivial" as political correctness??

It bugs me that you can kill Datadyne and Area 51 guards with impunity, but not NSA agents. It makes sense that the NSA guys would be spared because they don't know what Easton is up to and thus are innocents who are just doing their jobs. Fine. Except that I doubt the Datadyne guards know all about their company's evil deeds; most likely, they just think it's involved in making robots or something, have no idea that Cassandra wants to take over the world, and are just keeping criminals from stealing valuable technology. Similarly, the Area 51 guards are government employees working to prevent foreign operatives, spies, and terrorists from stealing information and technology that could potentially bring down America.

Carrington doesn't seem like such a swell guy when you think about it.

- Initial Vector portrays him as a man at war against Data Dyne and the Mega Corps, and is fairly jaded, cynical and ruthless. Plus I might be mistaken, but those after Jo I believe were NSA agents with Trent and the snow guards and Presidential security are rank and file US employees. The guards won't go after you when you are face to face with the President, and they'll go off and fight the invading NSA if spared. Area 51 though, that is morally ambiguous.